Search Results (323)

Listeria monocytogenes is already a well-known foodborne bacterial pathogen, ubiquitously dispersed not only in the food production environment but also in the primary animal production environment as well. The present study performed whole-genome characterization of the multidrug-resistant (MDR) L. monocytogenes strain BF11, previously isolated from raw pet food and phenotypically described for antimicrobial resistance. To this end, the genomic analysis performed on the isolate confirmed the pathogen’s designation as a serotype 1/2b strain belonging to ST5 and CC5 (Lineage I), carrying multiple MDR genes, stress-related genes, and mobile genetic elements, despite the absence of plasmids. The strain is phylogenetically closely related to Lineage I epidemic strains (e.g., F2365), as it has a full-length inlA and a functional prfA, rendering it capable of invading human cells and marking its high virulence. Overall, this strain may represent a potentially novel genomic profile when core genome multilocus sequence typing (cgMLST) is used, although further data from additional isolates would be required to confirm its classification within a new Complex Type, while displaying a hybrid unique profile. It is an evolved ST5 L. monocytogenes strain that has acquired genetic material conferring a “clinical signature” (Lineage I-like) and an extensive resistance network. Therefore, presence of L. monocytogenes strain BF11 in pet food is alarming, since such hybrid strains often evade surveillance monitoring as they do not fit strictly into classical categories, posing a serious food safety and public health threat in the concept of One Health. Full article

Conservation tillage has an influence on the cultivation and sustainable utilization of farmland. However, the microbial mechanism driving soil nutrient cycling in conservation tillage and its regulation pathway remain unclear. Based on a positioning experiment in black soil areas, this study systematically compared the effects of no-tillage (NT) and moldboard tillage (MT) combined with different straw returning amounts (straw non-returning, NS; straw half-returning, HS; straw full-returning, TS) on the composition of soil carbon (C), nitrogen (N) and phosphorus (P) and focused on the role of microbial community structure succession and functional changes in soil nutrient cycling. Microbial community remodeling driven by tillage measures was mainly regulated by C and N components. Bacterial modules 2 and 4 and fungal modules 1 and 2 were key for regulating the C, N and P cycle, of which 87 bacteria and 45 fungi taxa represented the core driving microorganisms. The total amount of no-tillage straw return reduced the formation and accumulation of labile organic carbon fractions by enriching yeast-like fungi and inhibiting the expression of complex organic matter decomposition genes. Tillage mainly promoted the accumulation of labile organic carbon fractions and nutrient release by regulating the bacterial community, while no-tillage straw returning promoted the accumulation of total organic carbon and organic nitrogen fixation by promoting the fungal community. This study revealed the biological pathway of conservation tillage that drives soil nutrient cycling by regulating key microbial communities. It also provides a microbiological basis for sustainable soil management in black soil areas. Full article

Monoculture plantations often face challenges of soil degradation and declining ecosystem services. Intercropping is beneficial to improving soil quality; however, the long-term effects of intercropping woody plants with medicinal herbs on soil ecosystems remain unclear. This study aimed to investigate the temporal effects of different durations of poplar intercropping with Aralia elata on soil physicochemical properties, enzyme activities, and soil microbial community structure. Soil samples were collected from the 0–20 cm soil layer, with composite samples obtained by mixing four soil cores per plot. We determined soil physicochemical properties, including pH, total carbon (TC), total nitrogen (TN), and total phosphorus (TP); soil enzyme activities, including invertase, urease, phosphatase, and β-N-acetylglucosaminidase (NAG); and soil microbial community structure using high-throughput sequencing of the bacterial 16S rRNA gene and fungal ITS region. Intercropping significantly affected soil chemical properties and enzyme activities in poplar plantations. Compared with the monoculture control (Y), TN (p < 0.01) and TC (p < 0.01) contents increased significantly in the 3- and 7-year intercropping treatments. The activity of β-N-acetylglucosaminidase (NAG) was enhanced following poplar–Aralia elata intercropping. In addition, intercropping significantly changed the composition and structure of soil microbial communities. In summary, introducing Aralia elata into poplar plantations can effectively improve soil fertility and reshape soil microbial community structure. This positive effect is time-dependent and becomes more significant with a 7-year intercropping duration. Poplar–Aralia elata intercropping represents a feasible management strategy to enhance ecological sustainability and soil health in plantation ecosystems of Northeast China. Full article

River sediment microbial communities are an integral part of fluvial ecosystems, where they play a central role in nutrient cycling. Although these communities share a core group of microorganisms, their overall composition can be influenced by natural environmental conditions and anthropogenic factors. While anthropogenic influences on river microbial communities have been extensively studied, natural drivers have received comparatively less attention. In this study, we evaluated the impact of tributary inflow on the microbial assemblages of a main river stem. Sediment samples were collected from both the main channel and some of its tributaries, and bacterial community composition was characterized using 16S rRNA gene amplicon sequencing. Taxonomic profiling revealed a largely shared core community typical of riverine sediments across all sites. While alpha diversity did not differ significantly between main river and tributary samples, beta diversity analyses demonstrated clear segregation between the two environments, indicating distinct community structures. Correlation analyses further showed that microbial assemblages in the main river downstream of tributary confluences were significantly associated with tributary community composition, highlighting the influence of tributary inflow on bacterial communities in the main river. Full article

Background: Epimedium is a natural herb with immunomodulatory potential, but its vaccine adjuvant properties remain poorly understood. Objective: The aim of this study was to elucidate the adjuvant effects of Epimedium and the underlying molecular mechanisms. Methods: Network pharmacology was used to identify bioactive compounds and targets of Epimedium from the TCMSP database, and immunomodulation-related targets from GeneCards and OMIM. PPI networks, KEGG/GO enrichment, molecular docking, and molecular dynamics (MD) simulations were performed. In vivo, female BALB/c mice were immunized with the Staphylococcus aureus (S. aureus) vaccine subunit HI antigen, either alone or with low- or high-dose icariin (ICA). Serum antibody responses (IgG, IgG1, IgG2a, IgG2b) were measured by ELISA. Survival against lethal S. aureus USA300 challenge was monitored. Results: Network pharmacology predicted 488 targets and 13 pathways. Core targets included IL6, TP53, EGFR, CTNNB1, HIF1A, HSP90AA1, JUN, MTOR, SRC, and AKT1. KEGG/GO analysis indicated involvement of T cell receptor and NOD-like receptor signaling pathways in inflammatory responses. Molecular docking and MD simulations confirmed stable ligand-target binding. Experimental validation showed that ICA significantly enhanced HI-specific antibody responses and induced a Th2-biased humoral immune response (IgG1/IgG2a ratio > 1), which is particularly relevant for vaccines targeting extracellular pathogens such as S. aureus. ICA also improved survival after lethal bacterial challenge. Conclusions: This study identifies potential bioactive compounds, core targets, and key pathways of Epimedium as a vaccine adjuvant. Experimentally, ICA, as a representative component, enhanced HI-specific antibody responses and conferred protection against lethal S. aureus challenge. Together, these findings offer a computational–experimental basis that may guide further mechanistic investigation. Full article

Background/Objectives: Staphylococcus aureus, particularly methicillin-resistant strains, is a leading cause of severe pneumonia. Understanding local molecular epidemiology, including virulence gene profiles and antimicrobial resistance (AMR) mechanisms, is crucial for effective infection control. This pilot study aimed to characterize S. aureus isolates from pneumonia patients in Karaganda, Kazakhstan. Methods: We collected 48 respiratory samples from patients with pneumonia across three medical institutions. Bacterial identification was performed using MALDI-TOF MS. Antimicrobial susceptibility testing (AST) was carried out using European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Whole-genome sequencing of S. aureus isolates was conducted on an Ion Torrent S5 platform. Genomic analysis included multilocus sequence typing (MLST), identification of virulence and AMR genes, and phylogenetic reconstruction. Results: S. aureus was identified in 14.6% (n = 7) of pneumonia cases included in this study. All isolates (100%, n = 7) were phenotypically resistant to benzylpenicillin. The mecA gene was detected in 57.1% of isolates (n = 4), while phenotypic resistance to methicillin was observed in 28.6% (n = 2) of the isolates. Resistance to azithromycin (57.1%, n = 4) and levofloxacin (42.9%, n = 3) was observed among the isolates. Two isolates (28.6%) were multidrug-resistant (MDR). Genomic analysis revealed the prevalence of the ST22 clone (57.1%, n = 4) in the studied cohort. Other sequence types were ST97, ST8, and ST45 (14.3% each). Phylogenetic analysis showed clustering consistent with MLST profiles. All isolates carried a conserved core virulence arsenal, including hemolysin (hla, hlg), biofilm-forming genes (icaADBC), immune evasion genes (sak, scn), and iron acquisition genes (isd). The Panton–Valentine leukocidin (PVL) genes were detected in three isolates. AMR gene analysis revealed the ubiquitous presence of mepA and tetracycline efflux pump genes, along with regulatory genes (arlRS, mepR, mgrA). The blaZ and ermA genes were not detected despite high phenotypic resistance to penicillin and macrolides. Conclusions: This study reports the identification of the virulent and resistant ST22 S. aureus clone in pneumonia cases in Karaganda, Kazakhstan. The discordance between phenotypic and genotypic AMR profiles underscores the necessity for integrated diagnostic approaches. Full article

This study investigated phase-dependent changes in gut microbiome composition, predicted functional potential, and lipid metabolism in intensively reared broiler chickens and ducks across the starter, grower, and finisher phases (from day-old to 42 days of age), over six production cycles (four chicken and two duck cycles), using 16S rRNA sequencing and blood lipids profiling. A total of 70 pooled manure samples were collected (46 from chickens and 24 from ducks), along with 34 blood samples (22 from chickens and 12 from ducks), all obtained under standard production conditions. Microbial diversity remained stable across growth phases within each species, whereas clear interspecies differences were observed (p < 0.01). Microbiome maturation involved a shift from early facultative and environmentally associated taxa during the starter phase (day-old to 14 days of age), including Acinetobacter (p < 0.01) and Enterococcus (p < 0.001), toward a more stable, host-adapted community. At the level of predicted functional pathways, shifts between growth phases were more pronounced in ducks. Predicted gene-level profiles showed phase-specific differentiation in chickens, with starter-associated genes linked to core carbon and nitrogen metabolism and finisher-associated genes related to structural and transport functions, whereas ducks exhibited a more balanced reorganization involving carbohydrate, energy, and nitrogen metabolism. Host lipid profiles between adjacent growth phases showed dynamic shifts in ducks (p < 0.05). These species-specific lipid patterns were mirrored by microbiome–lipid associations, as demonstrated by correlation analyses between dominant bacterial genera and blood lipid parameters, revealing more coordinated relationships in chickens and more heterogeneous patterns in ducks. Overall, these findings demonstrate species-specific organization of gut microbiome changes and their integration with blood lipid profiles under intensive production conditions. Full article

Pasteurella multocida (P. multocida) is not only the core pathogen of bovine respiratory disease (BRDC) but also a significant zoonotic agent, posing a dual threat to global animal husbandry and public health. This study utilized untargeted metabolomics to systematically dissect the metabolic regulatory network of P. multocida in response to tylosin within a One Health framework. The results revealed significant “defense–growth” metabolic reprogramming: activation of amino sugar and nucleotide sugar pathways (e.g., CDP-glucose) indicated cell wall remodeling, while directional shifts in the phenylalanine–tyrosine network directed flux toward defensive secondary metabolites. Concurrently, amino acid disorders and the overactivation of the ABC transporter system exacerbated an internal energy crisis, characterized by a shift from respiration to glycolysis, ATP depletion, and ROS accumulation. SEM observations confirmed membrane integrity disruption and cytoplasmic leakage. Crucially, this metabolic stress and the transition into a “persister-like” dormant state are closely linked to the adaptive expression of antimicrobial resistance (AMR) genes. Under the selective pressure of tylosin, these metabolic perturbations may facilitate the emergence and horizontal transfer of resistance determinants, which can circulate through the animal–human–environment interface. By revealing the metabolic physiological basis of tylosin’s action and its role in inducing bacterial tolerance, this study provides critical theoretical insights for antimicrobial stewardship, aiming to mitigate the risk of AMR transmission and preserve the efficacy of macrolides for both veterinary and human medicine. Full article

Environmental pH plays a critical role in microbial fermentation processes. Weizmannia coagulans attracts particular attention for exceptional acid tolerance and lactic acid productivity. Yet acidic stress impacts on its cell division regulation remain unclear. Here, a critical pH value (pH 4.20) for growth inhibition of the Gram-positive bacterium Weizmannia coagulans strain BC99 was first established. Transcriptomic analysis of metabolic pathways was then performed. The multi-layered regulatory network underlying acid stress-induced cell division was elucidated. Integrated transcriptomic and physiological analyses reveal that acid stress triggers multigene expression reprogramming. This drives core metabolic network reorganization, coordinately regulating division processes. RNA-seq analysis demonstrated acid stress triggered differential expression of division genes (FtsZ/Q downregulation), ATP synthase suppression, and peptidoglycan transport reduction, while enhancing membrane rigidification (Cfa) and magnesium homeostasis (CorA). The PhoPR dual-component system emerged as a central regulator, inhibiting septal assembly via RipA hydrolase and RpsU ribosomal suppression while rerouting carbon flux to glycolysis, elucidating bacterial acid adaptation mechanisms. Collectively, these adaptive changes prioritize cell survival over active proliferation under acidic conditions. This study provides molecular insights into how W. coagulans preserves viability under acid stress, offering a theoretical basis for optimizing its performance in probiotic applications. Full article

The genus Listeria comprises diverse bacteria with significant public health relevance, particularly Listeria monocytogenes. A comparative genomic analysis of ten representative Listeria species was conducted using 33 high-quality genome assemblies to investigate core and accessory genome dynamics and identify candidate diagnostic loci. Pangenome reconstruction was performed using the Roary Integer Linear Programming Bacterial Annotation Pipeline (RIBAP) to classify core, soft-core, and accessory genes, while average nucleotide identity (ANI) analysis assessed genomic relatedness across thresholds of 60–95%. Functional annotation of core and species-specific genes was conducted using Genome Annotation and Information Analysis (GAIA). Core genes were highly conserved and associated with essential cellular functions, whereas the accessory genome contributed to species-level diversification and ecological adaptation. Candidate molecular markers were derived from accessory genes and evaluated based on presence/absence across genomes, retaining loci present in ≥80% of target strains and absent in non-target strains. Experimental validation of selected primers was performed using two L. monocytogenes reference strains (ATCC 19117 and ATCC BAA-679) with conventional PCR and gel electrophoresis to confirm expected amplicon sizes and specificity. These findings establish a genome-informed, specificity-driven framework for marker development and highlight the accessory genome as a valuable source of diagnostic loci, supporting accurate detection, epidemiological surveillance, and food safety monitoring. Full article

Although peanut shells represent an abundant agricultural waste, their high-value utilization potential as a horticultural substrate has not been fully recognized. Meanwhile, horticultural crops such as tomatoes are in urgent demand for high-quality and innovative cultivation substrates. This study investigated the effects of different ratios of peanut shell–substrate on tomato yield and rhizosphere bacterial community structure, aiming to provide a theoretical basis for the utilization of agricultural waste and the development of novel growth substrates for tomato cultivation. Results showed that peanut shell–substrate improved tomato yield and quality, and enhanced soil urease, sucrase, and catalase activities. High-throughput 16S rRNA gene sequencing revealed significant differences in rhizosphere bacterial alpha diversity between peanut shell substrates and the control. Proteobacteria, Acidobacteria, and Actinobacteriota were the dominant phyla, while unclassified genera, Devosia A_501803 and Bauldia, were identified as the core genera at the genus level. In conclusion, peanut shell substrates enriched dominant functional bacterial genera and enhanced the ecological functions of the substrate. Full article

As the predominant native pollinator across Asia, Apis cerana is essential for the maintenance of biodiversity and agricultural productivity. The gut microbiota of honeybees plays a central role in host nutrition, detoxification, and immune function. p-Coumaric acid, a widespread phenolic acid enriched in pollen and nectar, has been reported to promote honeybee health by prolonging lifespan and increasing the expression of detoxification-related genes, hence improving tolerance to pesticides. Its influence on gut microbial communities, however, remains insufficiently characterized in A. cerana. This study evaluated the effects of dietary p-coumaric acid on survival, sucrose solution consumption, and gut microbiome composition in A. cerana workers using absolute quantification sequencing. Bees were provided sucrose solutions containing p-coumaric acid at concentrations of 41.0, 82.0, and 164.0 mg/L for durations of 5 and 10 days. The results indicated no effect on survival but revealed time-dependent changes in sucrose solution consumption. p-Coumaric acid exposure altered the abundance of non-core bacterial taxa, including Bombella and Apilactobacillus, whereas the core gut microbiota (Lactobacillus, Gilliamella, Snodgrassella, Apibacter, and Bifidobacterium) remained stable. These results suggest that p-coumaric acid modulates sucrose solution consumption and selectively influences non-core gut bacteria without disrupting survival or core microbiota stability, underscoring its role in regulating host–microbe interactions in honeybees. Full article

Promoting the agricultural recycling of biogas slurry (BS) is crucial for sustainable development, yet its long-term ecological impacts remain unclear. Through a multi-year field trial in a sugarcane system, this study examined the effects of BS application (0, 3, and 6 years) on the soil properties, bacterial communities, and functional genes for C, N, P, and S cycling. The results revealed distinct two-phase patterns of changes in soil properties, microbial communities, and functional genes. Short-term (3-year) application induced a “disturbance” phase, characterized by significant acidification (pH decreased by 17.91%), a surge in nitrate-N (increased by 757.27%), and a transient decline in bacterial richness. Long-term (6-year) application drove a “functional restructuring” phase, reversing acidification and significantly increasing soil organic matter (29.05%) and total nitrogen (TN) (20.81%). Bacterial richness recovered, and community composition distinctively restructured. Functional gene analysis revealed shifts in gene abundance that transitioned from high abundance in the short term to a new balance favoring processes like N fixation. Co-occurrence network analysis indicated that this functional shift was associated with core microbial modules (e.g., Firmicutes) and changes in soil pH and SOM. This study suggests that, although short-term application causes significant adjustments, sustained and appropriate BS application can ultimately enhance soil fertility and promote a functionally reorganized state by reshaping microbial interaction networks. It presents a microbial ecological basis for the safe and sustainable use of BS in circular agriculture. Full article

Helicobacter pylori (H. pylori) is the primary etiological agent for chronic gastritis, peptic ulcers, and gastric adenocarcinoma. The alarming rise in multidrug-resistant (MDR) strains, particularly against clarithromycin (CLR), metronidazole (MNZ), and levofloxacin (LVX), has severely compromised standard therapies. Thus, there is an urgent clinical need for novel antimicrobial agents that operate through distinct mechanisms to bypass resistance pathways and mitigate gastric cancer risk. We designed and synthesized a series of antimicrobial peptides, focusing on the proteolytically stable all-D-amino acid enantiomer, DT7-3, derived from a probiotic-sourced template. Minimum inhibitory concentrations (MICs) were determined against standard strains and 11 clinical MDR isolates via the broth microdilution method. Antimicrobial mechanisms were elucidated using scanning electron microscopy (SEM) for morphology, fluorescence-based assays for anti-adhesion activity, and real-time qPCR to quantify virulence gene expression (babA, ureA, and vacA). Biocompatibility was assessed using defibrinated sheep erythrocytes, gastric epithelial cells (GES-1), and representative beneficial gut microbiota. Analysis of the clinical isolates revealed resistance rates of 63.6% for CLR/LVX and 81.8% for MNZ, with 54.5% identified as MDR. DT7-3 exhibited superior potency (MIC 1–32 µg/mL) against all strains, significantly outperforming its L-enantiomer counterparts. Mechanistic studies unveiled a “triple-hit” mechanism: (1) rapid membrane disruption; (2) potent inhibition of bacterial adhesion to host cells (~60% reduction at 0.5 × MIC); (3) significant downregulation of critical virulence factors (babA, ureA, and vacA). Furthermore, DT7-3 showed an excellent safety profile, with negligible hemolysis (<5% at 32 µg/mL) and minimal cytotoxicity toward GES-1 cells, yielding a high selectivity index (SI, MHC/MIC) > 32 relative to mammalian cells. Crucially, DT7-3 showed high selectivity for the pathogen over beneficial gut microbiota (MIC > 128 µg/mL, SI > 16). Crucially, DT7-3 maintained potent bactericidal activity (MIC ≤ 16 µg/mL) even under cholesterol-enriched conditions. The engineered D-peptide DT7-3 is a potent candidate for combating MDR H. pylori. Its multifaceted mechanism, targeting bacterial viability while suppressing core virulence factors, positions it as a robust lead compound for next-generation eradication therapies aimed at reducing the burden of H. pylori-associated diseases. Full article

The gut microbiota is a crucial component of a tiger’s health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles. Full article