Search Results (58)

Staphylococcus aureus is an important zoonotic pathogen that threatens public health, food safety, and livestock production. Bacteriophages are promising antibacterial agents for controlling antimicrobial-resistant S. aureus, but their biological properties and genomic safety require systematic evaluation. In this study, three S. aureus phages, vB_SauL_202501, vB_SauM_202502, and vB_SauL_202503, were isolated from sewage samples and characterized by morphological observation, biological assays, whole-genome sequencing, and phylogenetic analysis. Transmission electron microscopy showed that vB_SauL_202501 and vB_SauL_202503 exhibited siphovirus-like morphology, whereas vB_SauM_202502 displayed myovirus-like morphology. Among the three phages, vB_SauM_202502 showed a relatively broader lytic spectrum and stronger sustained lytic activity in the spot assay. The optimal multiplicities of infection were 0.1, 0.1, and 0.01, respectively, and vB_SauL_202503 showed the shortest latent period, approximately 30 min. All three phages retained detectable infectivity at pH 5–10 and 4–37 °C, while vB_SauM_202502 maintained relatively high residual titers after heat treatment and ultraviolet irradiation. Genome analysis revealed double-stranded DNA genomes of 43,180–44,630 bp with GC contents of approximately 33.5%. No typical antimicrobial resistance genes or definitive auxiliary metabolic genes were identified. However, genes associated with lysogenic regulation, recombination, or immune modulation were detected in some phages, indicating that their lifestyles and application safety require further validation. These findings enrich S. aureus phage resources and provide a basis for the comparative characterization and safety assessment of candidate phages. Full article

Background: The bean flower thrips, Megalurothrips usitatus, is a destructive agricultural pest with increasing resistance to pyrethroid insecticides. Most mechanistic studies emphasize mutations in the pore-forming voltage-gated sodium channels α-subunit, whereas the contribution of insect-specific sodium-channel auxiliary subunits remains unclear. Methods: We used dsRNA feeding, pyrethroid bioassays, RNA sequencing, and RT-qPCR validation to evaluate the role of temperature-induced paralytic E (TipE) in M. usitatus. Results: The optimized RNAi condition was 400 μg/mL of dsTipE for 48 h, which reduced TipE expression by 32.55%. TipE knockdown increased adult mortality after exposure to λ-cyhalothrin and permethrin, indicating increased pyrethroid-associated susceptibility under laboratory conditions. Transcriptome sequencing identified 205 differentially expressed genes, with enrichment in metabolism-related pathways. RT-qPCR confirmed reduced expression of CYP307a1, an ecdysteroid-biosynthesis-related P450 gene, and SCD, a lipid-metabolism gene, while Na_v α-subunit transcript abundance did not change significantly. Conclusions: These results identify TipE as an auxiliary-subunit factor associated with pyrethroid susceptibility in M. usitatus and provide a transcriptome-based working model linking sodium-channel auxiliary regulation with endocrine- and lipid-metabolism-related responses. This study expands the candidate space for pyrethroid resistance research beyond Na_v α-subunit mutations, although the causal roles of CYP307a1 and SCD require further validation. Full article

Background: Colorectal cancer (CRC) is driven by genetic alterations, epigenetic dysregulation and tumor microenvironment remodeling. Histone modification reader proteins serve as key epigenetic regulators of anti-tumor immunity, yet their synergistic immune networks, combined prognostic roles and immune subtype heterogeneity remain poorly understood. Methods: Here, we integrated multi-omics data and graph attention networks (GAT) to systematically screen prognostic-associated histone reader genes. We then conducted analyses using the immunoassay pipeline and ultimately identified hub immune-related genes validated in independent external cohorts. Additional analyses, including single-cell RNA sequencing (scRNA-seq), molecular docking and multiple in silico functional assays, were performed based on retrospective public datasets. Results: Four core genes (CUL7, GPC1, NFYA, SLC25A5) exhibited robust prognostic performance and strong correlations with anti-tumor immunity. Both core and auxiliary genes participate in critical metabolic and immune pathways. Candidate drugs present differential binding affinity for their encoded proteins, with sapitinib designated as a promising agent. Conclusions: This work constructs an epigenetic immune regulatory network and a four-gene signature, offering promising biomarkers and actionable therapeutic targets for precision immunotherapy against CRC. Full article

Despite extensive research on biochar’s effects on soil properties, the molecular mechanisms linking carbon-cycling functional genes to soil organic carbon dynamics under biochar application remain poorly understood. This study evaluated the effects of corn stalk biochar applied at different rates (0, 300, 600, and 900 kg/hm²) on soil physicochemical properties, microbial community structure, carbon cycling genes, and soybean (HeiNong551) growth in Northeast China’s black soil region. Metagenomic analysis and metabolic pathway analysis were also conducted. Biochar application significantly improved soil fertility by increasing pH, moisture content, and various SOC fractions, while modulating the activities of key soil enzymes, including β-glucosidase, alkaline phosphatase, cellulase, and polyphenol oxidase. Metagenomic analysis revealed that biochar substantially enhanced soil microbial richness and diversity, with significant enrichment of beneficial bacterial genera, including Nocardioides and Sphingomicrobium. Functional gene analysis demonstrated that biochar promoted soil carbon cycling by increasing the abundance of Glycosyltransferases, Glycoside Hydrolases, and Auxiliary Activities, while decreasing the abundance of Carbohydrate-Binding Modules, Carbohydrate Esterases, and Polysaccharide Lyases. Analysis of 22 key carbon cycling pathway genes indicated that biochar enhanced carbon fixation via the reductive tricarboxylic acid cycle (korA gene) and promoted the degradation of easily mineralizable SOC components, while suppressing stable carbon degradation pathways. Full article

Hypsizygus marmoreus (Peck) H.E. Bigelow is a commercial edible mushroom includes two primary commercial varieties: brown and white. To reveal the genetic and metabolic differences between these two varieties, genomic and metabolomic comparisons of the white strain F4 and the brown strain B5-15 were performed. The assembled genome sizes were 40,851,948 bp for F4 and 41,902,673 bp for B5-15. Molecular clock analysis estimated that H. marmoreus diverged from Termitomyces sp. approximately 59.4 million years ago during the Paleocene based on the genomic information. The two genomes showed little difference in the gene compositions related to β-Glucosidase and certain lignin degrading auxiliary enzymes. In contrast, the structures of the mating-type loci, including gene copy numbers and the transcriptional orientation of open reading frames, differed between the varieties, and it exhibited higher mating-type locus diversity. Comparative genomic analysis further indicated that the brown strain can biosynthesize melanin-like compounds using chorismate as the starting molecule, with tyrosinase acting as a key enzyme. Moreover, metabolomic profiling based on principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) revealed distinct metabolic profiles between the two varieties. Collectively, these findings improve our understanding of the genetic basis underlying the phenotypic differences between the two H. marmoreus varieties. Full article

Goose blood has anticancer properties and was recorded in ancient China, but the specific molecular mechanisms underlying this effect still require further exploration. In this study, SW1990 cells were treated with goose serum or plasma, and transcriptome analysis was performed to explore the function of goose blood on cancer cells. Metabolomic profiling was also performed on goose serum, goose plasma, chicken serum, and chicken plasma to identify the bioactive substances responsible for the anticancer effect. The study examined the effects of goose plasma and serum on SW1990 cells and compared the metabolites between goose and chicken blood. Wound scratch, CCK-8, and Annexin V-PI assays showed that goose plasma and serum inhibited SW1990 cell proliferation at 24 and 48 h. Both treatments reduced cell viability, with serum inducing early and late apoptosis and plasma inducing late apoptosis. RNA sequencing (RNA-seq) identified 2259 (1418 upregulated, 841 downregulated) and 2731 (1844 upregulated, 887 downregulated) differentially expressed genes (DEGs) in the plasma and serum groups versus the negative control (NC), respectively, and 689 DEGs between the plasma and serum groups. Gene Ontology (GO) and KEGG pathway analyses revealed that the DEGs were enriched in processes such as lipid metabolism, JAK-STAT, and IL-17 pathways. Untargeted liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis identified distinct metabolites in goose and chicken blood, with unique metabolites and differential ones between groups. In SW1990 cells, four metabolite subclusters matched the plasma and serum effects. In summary, goose blood can suppress cancer cells by regulating gene expression to affect the key signaling pathways involved in cancer cell apoptosis and autophagy. Certain metabolites present at high concentrations in goose blood, such as cucurbitacin D and Oleoyl-L-carnitine, may also contribute to the inhibition of cancer cell proliferation and migration. These findings suggest that goose blood holds broad application prospects as a future auxiliary drug for cancer treatment, and this study provides a theoretical basis for the further application of goose products. Full article

Members of the class Campylobacteria are microaerophilic bacteria widely distributed across diverse environments and are abundant in hydrothermal systems. However, cultivated representatives, particularly from shallow-water vents, remain limited. Here, we investigated the genomic diversity and environmental adaptation of the genus Sulfurospirillum. Phylogenomic analysis revealed a clear separation between terrestrial and marine clades, with relatively few cultured representatives in the marine lineage. Strain 1307, isolated from shallow-water hydrothermal vents, expands the genomic representation of this underexplored clade. Pan-genome analyses based on complete genomes revealed an open pan-genome, indicating ongoing diversification of genus Sulfurospirillum. Further comparison between hydrothermal vent (HTV) and non-HTV lineages identified distinct adaptive features. Vent-associated strains are enriched in genes involved in sulfur metabolism, carbon fixation, the glycine cleavage system (GCS), and the biosynthesis of key cofactors (spermidine, thiamine, lipoate, and heme), reflecting metabolic adaptation to hydrothermal environments. Beyond well-established processes such as sulfur metabolism and autotrophic carbon fixation, the widespread presence of the GCS in vent-associated lineages suggests its potential role as an auxiliary carbon fixation pathway under anaerobic conditions. Overall, this study expands the phylogenetic and genomic diversity of Sulfurospirillum and offers new insights into the mechanisms underlying environmental adaptation and niche differentiation in vent-associated Campylobacteria. Full article

Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October–December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential. Full article

Low-density polyethylene (LDPE) and poly (butylene adipate-co-terephthalate) (PBAT) agricultural films are major components of microplastics (MPs) and their contamination in agriculture due to their difficulty to recycle. However, potential degradation mechanisms of MPs from LDPE and PBAT in agricultural soils are still unclear. Here, we isolated a strain of Bacillus cereus L6 from long-term agricultural MP-contaminated soil and analyzed its potential biochemical pathways involved in LDPE and PBAT turnover through functional prediction from shotgun genome sequencing. After 28 days of incubation with MPs, Bacillus cereus L6 caused a net mass loss of 0.99% LDPE-MPs/28 days and 3.58% PBAT-MPs/28 days. The surfaces of LDPE and PBAT degraded in bioassays added with Bacillus cereus L6 showed wrinkles, cracks, and pits, accompanied by an increase in roughness. The crystallinity and thermal stability of both LDPE- and PBAT-MPs were decreased and the hydrophobicity of PBAT-MPs was reduced. Whole-genome sequencing analysis showed that Bacillus cereus L6 potentially encoded genes for enzymes related to the biodeterioration of additives in LDPE and PBAT. Moreover, genomic CAZymes predictive analysis showed that genes related to oxygenases and lyases were annotated in the strain L6 Auxiliary Activities family. These findings offer a theoretical foundation for deeper exploration into the degradation and metabolic processes of MPs from discarded agricultural plastics in the environment. Full article

Lignin is one of the primary biomass resources in nature; however, its highly stable structure makes it difficult to degrade and utilise. As efficient decomposers of lignocellulosic biomass, termites rely on their gut microbiota for digestion. Consequently, termite guts harbour abundant and specialized lignin-degrading microorganisms. In this study, we isolated a bacterium from the termite gut and identified it as Bacillus cereus BC-8. The laccase activity of B. cereus BC-8 reached the maximum of 87.8 U/L at 72 h, and the lignin degradation rate reached 33.66% within 7 days. Furthermore, we analyzed the structural changes in lignin after treatment with this bacterial strain. Field emission scanning electron microscopy observations revealed that the surface structural integrity of lignin was significantly disrupted after treatment. Fourier transform infrared spectroscopy analysis indicated that B. cereus BC-8 affected the side chains and aromatic skeleton structures of lignin. Thermogravimetric analysis further revealed that B. cereus BC-8 disrupted the primary inter-unit β-O-4 ether bonds of lignin. Whole-genome sequencing of B. cereus BC-8 revealed a genome length of 5,374,773 bp and a GC content of 35.34%. Functional gene annotation revealed that the B. cereus BC-8 genome contains genes encoding various lignin-degrading enzymes (laccase, cytochrome P450, and vanillin oxidase) and their auxiliary factors, along with the phenylalanine and benzoic acid metabolic pathways, which are associated with lignin degradation. In conclusion, B. cereus BC-8 can break down the side chains, aromatic skeletons, and β-O-4 ether bonds of lignin molecules, demonstrating excellent lignin degradation ability. At the molecular level, this study elucidates the key genes and metabolic pathways related to lignin degradation in the genome of B. cereus BC-8. Full article

Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, including P. syringae. In an undergraduate lab course, P. putida was used as the host to isolate novel anti-pseudomonal bacteriophages. Environmental samples of soil and water were collected, and purified phage isolates were obtained. After Illumina sequencing, genomes of these phages were assembled de novo and annotated. Assembled genomes were compared with known genomes in the literature and GenBank to identify taxonomic relations and to refine their functional annotations. The thirteen phages described are sipho-, myo-, and podoviruses in several families of Caudoviricetes, spanning several novel genera, with genomes ranging from 40,000 to 96,000 bp. One phage (DDSR119) is unique and is the first reported P. putida siphovirus. The remaining 12 can be clustered into four distinct groups. Six are highly related to each other and to previously described Autotranscriptaviridae phages: Waldo5, PlaquesPlease, and Laces98 all belong to the Waldovirus genus, whereas Stalingrad, Bosely, and Stamos belong to the Troedvirus genus. Zuri was previously classified as the founding member of a new genus Zurivirus within the family Schitoviridae. Ebordelon and Holyagarpour each represent different species within Zurivirus, whereas Meara is a more distantly related member of the Schitoviridae. Dolphis and Jeremy are similar enough to form a genus but have only a few distant relatives among sequenced phages and are notable for being temperate. We identified the lysis cassettes in all 13 phages, compared tail spike structures, and found auxiliary metabolic genes in several. Studies like these, which isolate and characterize infectious virions, enable the identification of novel proteins and molecular systems and also provide the raw materials for further study, evaluation, and manipulation of phage proteins and their hosts. Full article

Viruses play a regulatory role in microbial ecology. Traditional fermented foods have complex fermentation environments with abundant viral participation, yet current research on viral communities in fermented foods remains insufficient. Traditional, manually produced solid-state fermented vinegar serves as an excellent model for studying the role of viral communities in fermented foods. Using metagenomic approaches, this study investigates the structure and dynamics of viral communities during the acetic acid fermentation process of Shanxi aged vinegar. All identified viruses were bacteriophages, and the dominant families were identified as Herelleviridae, Autographiviridae, and Stanwilliamsviridae. The richness and diversity of viral communities exhibited significant variations during acetic acid fermentation. Furthermore, correlation analysis revealed a strong association (p < 0.01) between core bacteria and core viruses. Functional annotation revealed the presence of viral genes associated with amino acid and carbohydrate metabolism. Notably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in viruses, with glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) demonstrating particularly high abundance. Additionally, several antibiotic resistance genes were detected in viruses. This study elucidates the impact of viral communities on microbial dynamics during food fermentation, advancing our understanding of viral roles in traditional fermented food ecosystems. Full article

Background/Objectives: Heparosan is a component of the capsular polysaccharide in Escherichia coli K5 and Pasteurella multocida Type D. It shares a similar glycan structure with heparin and can be enzymatically modified to produce bioactive heparin. Methods: In this study, the probiotic strain E. coli Nissle 1917 (EcN), which naturally produces heparosan, was genetically engineered to utilize sucrose as a carbon source for growth while achieving high-yield heparosan biosynthesis. Results: By expressing the sucrose hydrolase genes sacA (from Bacillus subtilis) or spI (from Bifidobacterium adolescentis), EcN was enabled to utilize sucrose, achieving heparosan titers of 131 mg/L and 179 mg/L, respectively. Further metabolic engineering was performed to block the glycolytic and pentose phosphate pathways, thereby redirecting sucrose-derived glucose-6-phosphate and fructose-6-phosphate toward heparosan biosynthesis, while glycerol was supplemented as an auxiliary carbon source to support cell growth. Finally, the key biosynthesis genes galU, kfiD, and glmM were overexpressed, resulting in an engineered strain with a heparosan titer of 622 mg/L. Conclusions: This study represents the first successful engineering of EcN to utilize sucrose as the carbon source for growth, while achieving enhanced heparosan production through synergistic carbon source utilization. These findings establish a foundational strategy for employing this strain in the sucrose-based biosynthesis of other glycosaminoglycans. Full article

Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety of biotechnological applications. Limnohabitans, with a ubiquitous distribution, is a metabolically versatile, fast-growing, morphologically diverse freshwater lake bacterial genera. It is especially abundant in pH-neutral and alkaline aquatic habitats, where it represents an average of 12% of freshwater bacterioplankton and plays an important role in funneling carbon from primary producers to higher trophic levels. However, no phages infecting Limnohabitans have been reported to date. Here, we describe, for the first time, three phages infecting Limnohabitans, DC31, DC33, and YIMV22061, isolated from two freshwater lakes in China and characterized using genome content analysis and comparative genomics. DC31 and DC33, recovered from the eutrophic Dianchi Lake, with auxiliary metabolic genes (AMGs), associated with nucleotide metabolism, whereas YIMV22061, isolated from the oligotrophic Fuxian Lake, carried AMGs involved in antibiotic resistance. The AMGs they carried highlight their impacts on Limnohabitans in different environments. Comparative genomic analyses indicate that DC31, DC33, and YIMV22061 represent three novel species in the Caudoviricetes class. IMG/VR database alignment further reveal that these phages are widely distributed across diverse aquatic and terrestrial ecosystems globally, suggesting their ecological significance. This study provides a basis for better understanding Limnohabitans–phage interactions. Full article

Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria–phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure. Full article