Search Results (1,775)

The gross benefit of feeding multi-species probiotics has been reported, but the effect on the gut microbiota in pre-weaned dairy calves has not been elucidated. To address this gap, a randomized controlled trial was conducted in California, USA, to investigate the effect of feeding probiotics on the fecal microbiota of pre-weaned dairy calves. A total of 30 neonatal calves were randomly assigned to either the probiotic (PRO) or control (CON) treatment. Fecal samples were collected at four age timepoints: days 7, 14, 21, and 42. Fecal bacterial population was analyzed using 16S rRNA amplicon sequencing. Differential abundance analysis was conducted to investigate the difference between the PRO and CON treatments, and diarrheic and non-diarrheic calves in each PRO and CON group. The PRO group had decreased Clostridium perfringens and Fusobacterium varium compared to the CON at 7 days of age. At 7 days of age, diarrheic calves in CON had more abundant F. varium compared to non-diarrheic calves, but there was no difference between diarrheic and non-diarrheic calves in the PRO group. In conclusion, probiotics administration decreased the population of pathogenic bacteria in feces from pre-weaned dairy calves on Day 7 of age. However, the treatment did not have an impact on bacterial diversity. These results suggest that the administration of probiotics has the potential to control gastrointestinal pathogens. Full article

Leather biodegradation is a complex microbial process with increasing relevance for sustainable waste management. In this study, we investigated bacterial communities responsible for the degradation of leather treated with different tanning agents (chrome, Zeolite, Biole^®) using high-throughput 16S rRNA gene sequencing and metatranscriptomic analysis. Proteobacteria, Bacteroidetes, and Patescibacteria emerged as the dominant phyla, while genera such as Acinetobacter, Pseudomonas, and Sphingopyxis were identified as key contributors to enzymatic activity and potential metal resistance. A total of 1302 enzymes were expressed across all the conditions, including 46 proteases, with endopeptidase La, endopeptidase Clp, and methionyl aminopeptidase being the most abundant. Collagen samples exhibited the highest functional diversity and total enzyme expression, whereas chrome-treated samples showed elevated protease activity, indicating selective pressure from heavy metals. Differential enzyme expression patterns were linked to both the microbial identity and tanning chemistry, revealing genus- and treatment-specific enzymatic signatures. These findings deepen our understanding of how tanning agents modulate the microbial structure and function and identify proteases with potential applications in the bioremediation and eco-innovation of leather waste processing. Full article

Fecal water syndrome (FWS) in horses is characterized by two-phase defecation, including both solid and liquid phases. While satisfactory explanations for FWS are unavailable, bacterial dysbiosis has been suggested as a contributing or causative factor. The objectives of this study were to determine whether fecal bacterial dysbiosis is associated with FWS in horses in the midwestern USA. Fecal samples were collected from horses with FWS and from unaffected horses at the same location. In total, 16S rRNA amplicon libraries produced from fecal bacterial DNA were sequenced using the Illumina sequencing platform. Significant differences in beta diversity were detected between affected and control horses (p = 7 × 10⁻⁴, F = 1.51), and differential abundance testing identified several features enriched in affected and control horses. These results agree with prior work regarding specific features in the bacterial microbiome associated with FWS, including Alloprevotella spp., and suggest fecal dysbiosis is associated with FWS. Full article

The rise of multidrug-resistant Pseudomonas aeruginosa underscores the need for novel therapeutic targets beyond conventional peptidoglycan biosynthesis. Some bacterial strains bypass MurA inhibition by fosfomycin via a cell wall salvage pathway. This study targeted P. aeruginosa AmgK (PaAmgK) and MurU (PaMurU) to identify inhibitors that could complement fosfomycin therapy. A malachite-green-based dual-enzyme assay enabled efficient activity measurements and high-throughput chemical screening. Screening 232 compounds identified Congo red and CTAB as potent PaMurU inhibitors. A targeted mass spectrometric analysis confirmed the selective inhibition of PaMurU relative to that of PaAmgK. Molecular docking simulations indicate that Congo red preferentially interacts with PaMurU through electrostatic contacts, primarily involving the residues Arg28 and Arg202. The binding of Congo red to PaMurU was corroborated further using SUPR-differential scanning fluorimetry (SUPR-DSF), which revealed ligand-induced thermal destabilization. Ongoing X-ray crystallographic studies, in conjunction with site-directed mutagenesis and enzyme kinetic analyses, aim to elucidate the binding mode at an atomic resolution. Full article

Acute hepatopancreatic necrosis disease (AHPND), caused by the bacterium Vibrio parahaemolyticus, is a major threat to global shrimp aquaculture. In this study, we evaluated the therapeutic effects of phage therapy in Litopenaeus vannamei challenged with AHPND-causing Vibrio parahaemolyticus. Phage application at various concentrations significantly improved shrimp survival, with the 1 ppm group demonstrating the highest survival rate. Enzymatic assays revealed that phage-treated shrimp exhibited enhanced immune enzyme activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), and lysozyme (LZM). In addition, antioxidant defenses such as superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-PX), and total antioxidant capacity (T-AOC) significantly improved, accompanied by reduced malondialdehyde (MDA) levels. Serum biochemical analyses demonstrated marked improvements in lipid metabolism, particularly reductions in triglyceride (TG), total cholesterol (TC), and low-density lipoprotein (LDL), alongside higher levels of beneficial high-density lipoprotein (HDL). Transcriptomic analysis identified 2274 differentially expressed genes (DEGs), notably enriched in pathways involving fatty acid metabolism, peroxisome functions, lysosomes, and Toll-like receptor (TLR) signaling. Specifically, phage treatment upregulated immune and metabolic regulatory genes, including Toll-like receptor 4 (TLR4), myeloid differentiation primary response protein 88 (MYD88), interleukin-1β (IL-1β), nuclear factor erythroid 2-related factor 2 (Nrf2), and peroxisome proliferator-activated receptor (PPAR), indicating activation of innate immunity and antioxidant defense pathways. These findings suggest that phage therapy induces protective immunometabolic adaptations beyond its direct antibacterial effects, thereby providing an ecologically sustainable alternative to antibiotics for managing bacterial diseases in shrimp aquaculture. Full article

The fungal component of microbiota, known as the mycobiome, inhabits different body niches such as the skin and the gastrointestinal, respiratory, and genitourinary tracts. Much information has been gained on the bacterial component of the human microbiota, but the mycobiome has remained somewhat elusive due to its sparsity, variability, susceptibility to environmental factors (e.g., early life colonization, diet, or pharmacological treatments), and the specific in vitro culture challenges. Functionally, the mycobiome is known to play a role in modulating innate and adaptive immune responses by interacting with microorganisms and immune cells. The latter elicits anti-fungal responses via the recognition of specific fungal cell-wall components (e.g., β-1,3-glucan, mannan, and chitin) by immune system receptors. These receptors then regulate the activation and differentiation of many innate and adaptive immune cells including mucocutaneous cell barriers, macrophages, neutrophils, dendritic cells, natural killer cells, innate-like lymphoid cells, and T and B lymphocytes. Mycobiome disruptions have been correlated with various diseases affecting mostly the brain, lungs, liver and pancreas. This work reviews our current knowledge on the mycobiome, focusing on its composition, research challenges, conditioning factors, interactions with the bacteriome and the immune system, and the known mycobiome alterations associated with disease. Full article

Ecological restoration in the cold and high-altitude mining areas of the Qinghai–Tibet Plateau is faced with dual challenges of extreme environments and insufficient microbial adaptability. This study aimed to screen local microbial resources with both extreme environmental adaptability and plant-growth-promoting functions. Local fungi (DK; F18-3) and commercially available bacteria (B0) were used as materials to explore their regulatory mechanisms for plant growth, soil physicochemical factors, microbial communities, and metabolic profiles in the field. Compared to bacterial treatments, local fungi treatments exhibited stronger ecological restoration efficacy. In addition, the DK and F18-3 strains, respectively, increased shoot and root biomass by 23.43% and 195.58% and significantly enhanced soil nutrient content and enzyme activity. Microbiome analysis further implied that, compared with the CK, DK treatment could significantly improve the α-diversity of fungi in the rhizosphere soil (the Shannon index increased by 14.27%) and increased the amount of unique bacterial genera in the rhizosphere soil of plants, totaling fourteen genera. Meanwhile, this aggregated the most biomarkers and beneficial microorganisms and strengthened the interactions among beneficial microorganisms. After DK treatment, twenty of the positively accumulated differential metabolites (DMs) in the plant rhizosphere were highly positively associated with six plant traits such as shoot length and root length, as well as beneficial microorganisms (e.g., Apodus and Pseudogymnoascus), but two DMs were highly negatively related to plant pathogenic fungi (including Cistella and Alternaria). Specifically, DK mainly inhibited the growth of pathogenic fungi through regulating the accumulation of D-(+)-Malic acid and Gamma-Aminobutyric acid (Cistella and Alternaria decreased by 84.20% and 58.53%, respectively). In contrast, the F18-3 strain mainly exerted its antibacterial effect by enriching Acidovorax genus microorganisms. This study verified the core role of local fungi in the restoration of mining areas in the Qinghai–Tibet Plateau and provided a new direction for the development of microbial agents for ecological restoration in the Qinghai–Tibet Plateau. Full article

Sepsis represents a major cause of mortality, especially among patients with liver cirrhosis, who are at increased risk due to immune dysfunction, gut-derived bacterial translocation, and altered hepatic metabolism. Traditional biomarkers such as C-reactive protein (CRP), procalcitonin (PCT), and interleukin-6 (IL-6) often have reduced diagnostic reliability in this subgroup, due to impaired liver and renal function. Presepsin, a soluble fragment of CD14 released during phagocytic activation, has emerged as a promising biomarker for early sepsis detection. This systematic review explores the diagnostic and prognostic utility of presepsin in cirrhotic and non-cirrhotic patients with suspected infection. Data from multiple clinical studies indicate that presepsin levels correlate with infection severity and clinical scores such as SOFA and APACHE II. In cirrhotic patients, presepsin demonstrates superior sensitivity and specificity compared to conventional biomarkers, maintaining diagnostic value despite hepatic dysfunction. Its utility extends to differentiating bacterial infections from fungal infections and monitoring treatment response. While preliminary evidence is compelling, further prospective, multicenter studies are required to validate its integration into standard care algorithms. Presepsin may become a valuable addition to clinical decision-making tools, particularly in hepatology-focused sepsis management. Full article

Fever is a frequent complication in children receiving chemotherapy, primarily caused by bloodstream infections and non-infectious inflammation. Yet, the pathophysiological mechanisms remain unclear, and diagnostics are insufficient, which often results in continued antibiotic treatment despite negative blood cultures. In a nationwide study, we collected whole blood in PAXgene tubes from 168 febrile episodes in children with hematological malignancies, including 37 episodes with bacteremia, and performed single-cell RNA sequencing. We compared transcriptomic profiles between febrile children with and without bacteremia. In children with bacteremia, differentially expressed genes were related to immunoregulation and cardiac and vascular function. Children without bacteremia had distinct gene expression patterns, suggesting a viral or other inflammatory cause of fever. Several differentially expressed genes overlapped with previously published transcriptomics-based diagnostic signatures developed in immunocompetent children. In conclusion, blood transcriptomics provided novel insights into the pathophysiological mechanisms of febrile children with hematological malignancies. We found differentially expressed genes suggesting viral infections or non-bacterial inflammation as causes of fever in children with negative blood cultures, supporting early antibiotic discontinuation in children with cancer. Full article

Understanding the distribution patterns of soil bacterial community structure and diversity across different forest types is essential for elucidating the mechanisms underlying microbial community assembly and its ecological drivers, particularly under the pressures of climate change. In this study, we examined six forest types—including four monocultures and two mixed-species stands—to systematically evaluate the structural composition, diversity metrics, and functional potential of soil bacterial communities. Significant differences in microbial structure and functional composition were observed among forest types. Mixed forests exhibited higher soil nutrient levels, more complex structures, and greater water retention capacity, resulting in significantly higher bacterial and functional diversity compared to monoculture forests. Bacterial diversity was greater in subsurface layers than in surface layers. Surface communities in monoculture forests showed relatively high structural heterogeneity, whereas deeper communities in mixed forests displayed more pronounced differentiation. The dominant bacterial phyla were mainly related to carbon and nitrogen metabolism, compound degradation, and anaerobic photosynthesis. Surface bacterial communities were primarily influenced by catalase activity, alkali-hydrolysable nitrogen, bulk density, and pH, whereas subsurface communities were largely controlled by pH, with supplementary regulation by nitrogen and potassium availability. Therefore, forest type and soil depth jointly influence the diversity, composition, and functional attributes of soil microbial communities by modulating soil physicochemical conditions. Full article

Triticale (Triticosecale Wittmack) is a versatile forage crop valued for its high yield, balanced nutrition, and environmental adaptability. However, the dough-stage triricale has higher dry matter and starch content but lower water-soluble carbohydrate levels than earlier stages, posing fermentation challenges that may impair silage quality. This study aimed to investigate the effects of lactic acid bacteria inoculation on the fermentation quality, bacterial community, and metabolome of whole-plant triticale silage at the dough stage. Fresh triticale was ensiled for 30 days without or with an inoculant containing Lactiplantibacillus plantarum and Streptococcus bovis. Fermentation quality, bacterial succession, and metabolic profiles were analyzed at multiple time points. Inoculation significantly improved fermentation quality, characterized by a rapid pH drop, increased lactic acid production, and better preservation of fiber components. Microbial analysis revealed that inoculation successfully established Lactobacillus as the dominant genus while suppressing spoilage bacteria like Enterobacter and Clostridium. Metabolomic analysis on day 30 identified numerous differential metabolites, indicating that inoculation primarily altered pathways related to amino acid and purine metabolism. In conclusion, inoculating dough-stage triticale with this LAB combination effectively directs the fermentation trajectory. It enhances silage quality not only by optimizing organic acid profiles and microbial succession but also by modulating key metabolic pathways, ultimately leading to improved nutrient preservation. Full article

There is a present need to develop alternative biotherapeutic drugs to mitigate the exacerbated inflammatory immune responses characteristic of sepsis. The potent endotoxin lipopolysaccharide (LPS), a major component of Gram-negative bacterial outer membrane, activates the immune system via Toll-like receptor 4 (TLR4), triggering macrophages and a persistent cascade of inflammatory mediators. Our previous studies have demonstrated that Fh15, a recombinant member of the Fasciola hepatica fatty acid binding protein family, can significantly increase the survival rate by suppressing many inflammatory mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a TLR4 antagonist, the specific mechanisms underlying its immunomodulatory effect remained unclear. In the present study, we employed a quantitative proteomics approach using tandem mass tag (TMT) followed by LC-MS/MS analysis to identify and quantify differentially expressed proteins that participate in signaling pathways downstream TLR4 of macrophages, which can be dysregulated by Fh15. Data are available via ProteomeXchange with identifier PXD065520. Based on significant fold change (FC) cut-off of 1.5 and p-value ≤ 0.05 criteria, we focused our attention to 114 proteins that were upregulated by LPS and downregulated by Fh15. From these proteins, TNFα, IL-1α, Lck, NOS2, SOD2 and CD36 were selected for validation by Western blot on murine bone marrow-derived macrophages due to their relevant roles in the NF-κB, iNOS, oxidative stress, and phagosome signaling pathways, which are closely associated with sepsis pathogenesis. These results suggest that Fh15 exerts a broad spectrum of action by simultaneously targeting multiple downstream pathways activated by TLR4, thereby modulating various aspects of the inflammatory responses during sepsis. Full article

Soil erosion-prone areas require effective microbial treatments to improve soil bacterial communities and functional traits. Understanding the driving effects of different microbial interventions on soil ecology is essential for restoration efforts. Single and combined microbial treatments were applied to soil. Bacterial community structure was analyzed via 16S IRNA high-throughput sequencing, and functional groups were predicted using FAPROTAX. Soil microbial carbon, nitrogen, metabolic entropy, and enzymatic activity were assessed. Microbial Carbon and Metabolic Activity: The Arbuscular mycorrhizal fungi (AMF) and Bacillus mucilaginosus (BM) (AMF.BM) treatment exhibited the highest microbial carbon content and the lowest metabolic entropy. The microbial carbon-to-nitrogen ratio ranged from 1.27 to 3.69 across all treatments. Bacterial Community Composition: The dominant bacterial phyla included Firmicutes, Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Diversity and Richness: The AMF and Trichoderma harzianum (TH) (AMF.TH) treatment significantly reduced diversity, richness, and phylogenetic diversity indices, while the AMF.BM treatment showed a significantly higher richness index (p < 0.05). Relative Abundance of Firmicutes: Compared to the control, the AMF, TH.BM, and TH treatments decreased the relative abundance of Firmicutes, whereas the AMF.TH treatment increased their relative abundance. Environmental Correlations: Redundancy and correlation analyses revealed significant correlations between soil organic matter, magnesium content, and sucrase activity and several major bacterial genera. Functional Prediction: The AMF.BM treatment enhanced the relative abundance and evenness of bacterial ecological functions, primarily driving nitrification, aerobic ammonia oxidation, and ureolysis. Microbial treatments differentially influence soil bacterial communities and functions. The AMF.BM combination shows the greatest potential for ecological restoration in erosion-prone soils. Full article

Background: Lycium chinense has been acknowledged for its substantial nutritional benefits. The “Mengqi No.1” variety of L. chinense is known for its high yield and exceptional quality. Methods: We screened twenty dominant endophytic bacterial genera based on OTUs from L. chinense fruits during three developmental stages. Results: Forty-three differential amino acid metabolites were selected from L. chinense fruits. Five endophytic bacteria (Enterococcus, Escherichia-Shigella, Bacteroides, Pseudomonas, and Bacillus) were dominant genera in green fruit (GF, 16–19 days after flowering), color-changing fruit (CCF, 22–25 days after flowering), and red-ripe fruit (RRF, 31–34 days after flowering). Four endophytic bacterial genera (Enterococcus, Bacillus, Pseudomonas, and Rhodanobacter) showed positive correlation with twenty different amino acid metabolites and negative correlation with seven different amino acid metabolites. Conclusions: Five genes (AST1, ltaE1, TAT1, SHMT2, and SHMT3) indicated positive correlation with seventeen different amino acid metabolites and negative correlation with eight different amino acid metabolites. AST1 gene had a major role in regulating arginine biosynthesis (ko00220); ltaE1, SHMT2, and SHMT3 genes were major in regulating glycine, serine, and threonine metabolism (ko00260); and TAT1 gene had a major role in regulating tyrosine metabolism (ko00350). These findings offer insights into the relationship between amino acid synthesis and endophytic bacteria in L. chinense fruits. Full article

Background/Objectives: Ascites is a major complication in patients with decompensated cirrhosis. Spontaneous bacterial peritonitis (SBP), an infection of the ascitic fluid, is a life-threatening condition in patients with cirrhosis. This study aimed to assess the utility of Tm mapping, a novel high-efficacy method for bacterial detection and quantification, in the early diagnosis of SBP and its pathogenesis. Methods: Ascitic fluid samples from 29 patients with cirrhosis were analyzed using Tm mapping for bacterial identification. Inflammatory cytokine and pathogen-associated molecular pattern levels in ascitic fluid were measured and correlated with SBP pathophysiology. Additionally, the role of ascitic macrophages was investigated in vitro. Results: Tm mapping detected bacteria more effectively than conventional culture methods. In samples where bacteria were identified, ascitic interleukin (IL)-6 levels were elevated. A positive correlation was observed between extracellular vesicle (EV) levels and IL-6, suggesting a role for EVs in peritoneal inflammation. Furthermore, EVs derived from Gram-negative bacteria induced M1 macrophage differentiation via the signal transducer and activator of transcription 1 signaling pathway. Conclusions: Tm mapping is a valuable tool for the early detection of bacteria in ascitic fluid. Additionally, EVs promote M1 macrophage differentiation, implicating them in the pathogenesis of cirrhotic complications, including SBP. Full article