Search Results (9,278)

Root-lesion nematodes of the genus Pratylenchus are among the most economically significant plant-parasitic nematodes worldwide. During nematological surveys conducted in natural and agricultural ecosystems in California, several known species, P. bolivianus, P. hippeastri, P. pinguicaudatus, P. scribneri, P. thornei, and P. vulnus, as well as two undescribed species, P. chizhovi sp. n. and P. gracilis sp. n., were recovered. Pratylenchus chizhovi sp. n. is characterized by a slightly offset lip region with three annuli narrowing anteriorly, a short stylet (14.5–17.0 µm) with rounded knobs, a lateral field with four incisures, a spherical spermatheca lacking sperm, a vulva with somewhat prominent lips, a subcylindrical tail with a truncate-rounded, smooth terminus, and unknown males. Pratylenchus gracilis sp. n. is characterized by a lip region offset with three annuli narrowing anteriorly, a short stylet (15–18 µm) with rounded knobs, a lateral field with four incisures, an oval to rounded spermatheca containing some sperm cells, a vulva with somewhat prominent lips, a subcylindrical tail with a rounded, smooth terminus, and males present. Phylogenetic relationships of California Pratylenchus species and other members of the genus were inferred using 18S rRNA, D2–D3 of 28S rRNA, and the mitochondrial COI gene sequences. This study provides an updated assessment of Pratylenchus species diversity in California, highlighting both previously described taxa and newly discovered species. Full article

Endophytic FoRo54 was isolated from the roots of Oryza rufipogon (Dongxiang wild rice) collected in China. Based on morphological characteristics and phylogenetic analysis of the 16S rRNA gene sequence, strain FoRo54 was identified as closely related to Micromonospora rosaria. The complete genome of FoRo54 consists of a linear chromosome of 7,057,852 bp with a GC content of 73.8 mol%. Genome mining using antiSMASH revealed 27 biosynthetic gene clusters (BGCs) potentially involved in secondary metabolite biosynthesis, including those associated with kanamycin, rosamicin, and asukamycin, consistent with the antibacterial activities of the strain. Application of a combined genome mining strategy enabled further exploration of the strain’s metabolic potential. One new rosamicin derivative, N-demethyl rosamicin (1), together with three known compounds, rosamicin (2), SCH 23831 (3), and tylactone (4), were isolated from fermentation broth. Antibacterial evaluation revealed that compounds 1-4 exhibited potent inhibitory activity against Staphylococcus aureus. Furthermore, based on genomic analysis, the biosynthetic pathway and putative gene functions responsible for these metabolites were proposed. Collectively, these findings highlight the metabolic versatility of the endophytic Micromonospora rosaria FoRo54, underscoring its potential as a valuable source of novel bioactive metabolites and providing a genomic framework for future heterologous expression and functional genetic characterization. Full article

Latex-producing plants harbor unique microbial communities that may play important roles in host defense; however, their diversity and biocontrol potential remain largely unexplored. Characterizing these communities provides opportunities to identify novel microbial-derived antifungal agents for sustainable crop protection. Bacterial strains were isolated from the latex of Alstonia scholaris (L.) R. Br. and identified using 16S rRNA gene sequencing. Antifungal activity was evaluated against four phytopathogens: Fusarium graminearum, Colletotrichum musae, Colletotrichum gloeosporioides, and Glomerella cingulata. Bioassay-guided fractionation, size-exclusion chromatography, SDS-PAGE, and LC-MS/MS were used to characterize antifungal proteins. Nine bacterial strains were isolated, including eight Bacillus spp. and one Enterococcus faecalis. Among them, Bacillus sp. AsL-2 exhibited the strongest broad-spectrum antifungal activity, inhibiting fungal growth by up to 80%. The antifungal activity of its crude extract remained stable over a wide temperature range. Further characterization identified a novel endo-β-1,3-1,4-glucanase enzyme (~23 kDa) as the major antifungal protein. This study reveals A. scholaris latex as an underexplored microbial niche and identifies Bacillus sp. AsL-2, affiliated with the B. velezensis–B. amyloliquefaciens species complex, as a promising biocontrol candidate. The identified antifungal enzyme represents a potential natural alternative to synthetic fungicides for sustainable agricultural disease management. Full article

In marine aquaculture environments, microplastics (MPs) and cadmium (Cd) are widespread contaminants that may jointly affect host–microbe interactions. Here, we examined the combined effects of MPs (5 mg/L) and Cd (5 μg/L) on the intestinal microbial community of pearl oysters after a 48 h exposure, followed by a 5-day recovery period. Gut microbiota dynamics were characterized using 16S rRNA gene sequencing. Alpha diversity did not vary significantly, whereas beta diversity showed marked alterations in community composition among the different exposure treatments. LEfSe analysis revealed distinct microbial biomarkers and putative pathogens under each treatment: Sulfitobacter in the MPs-alone group; Vibrio and Candidatus_Megaira in the Cd-alone group; and Tenacibaculum, Roseibacillus, and Enterovibrio across different co-exposure and recovery groups. A brief recovery period partially decreased the abundance of certain pathogens (e.g., Vibrio), yet some taxa (e.g., Enterovibrio and Tenacibaculum) remained enriched. These results indicate that exposure to MPs and Cd, whether alone or in combination, disrupts gut microbial homeostasis in pearl oysters by reshaping community structure and promoting the proliferation of potential pathogens, with some disturbances persisting after exposure ceases. Generally, our findings will aid evaluation of the ecological risks of combined pollutants in marine aquaculture systems. Full article

Analysis of pulmonary vascular dysfunction in various lung pathologies remains challenging due to the lack of functional ex vivo models. Paracrine signaling in the lung plays a critical role in regulating endothelial maturation and vascular homeostasis. Previously, we employed single-cell RNA-sequencing (scRNAseq) to systematically map ligand–receptor (L/R) interactions within the lung vascular niche. However, the functional impact of these ligands on endothelial biology remained unknown. Here, we systematically evaluated selected ligands in vitro to assess their effects on endothelial barrier integrity, anti-inflammatory responses, and phenotypic maturation. Among the top soluble ligands, we found that adrenomedulin (ADM) exhibited superior barrier enhancing effect on human pulmonary endothelial cell monolayers, as evidenced by electrical cell impedance sensing (ECIS) and XperT assays. ADM also exhibited anti-inflammatory properties, decreasing ICAM1 and increasing IkBa expression in a dose-dependent manner. Perfusion is commonly used in bioengineered vascular model systems. Shear stress (15 dynes/cm²) alone increased endothelial characteristics, including homeostatic markers such as CDH5, NOS3, TEK, and S1PR1. ADM treatment maintained the enhanced level of these markers under shear stress and further improved anti-coagulation by increasing THBD and decreasing F3 expression and synergistically enhanced the expression of the native lung aerocyte capillary endothelial marker EDNRB. This effect was completely attenuated by a blockade of ADM receptor, RAMP2. Together, these findings identify ADM/RAMP2 signaling as a key paracrine pathway that enhances vascular barrier integrity, anti-inflammatory phenotype, and endothelial homeostasis, providing a framework for improving the physiological relevance of engineered vascular models. Full article

Marine sponges are known to be associated with diverse and functionally specialized microbial consortia that are implicated in host metabolism, biogeochemical cycling, and bioactive compounds production. The microbiome diversity and composition of nine sponge species from the remote waters of Gageodo Island, Korea, were evaluated via full-length 16S rRNA sequencing and bioinformatic analyses. Each sponge species harbored a distinct microbial community, with differences potentially influenced by ecological factors, evolutionary history, and host–symbiont associations. The dominant microbial phyla identified across the sponge samples include Pseudomonadota, Cyanobacteriota, Acidobacteriota, Planctomycetota, and Chloroflexota, which were widely distributed across samples. In addition, the classes Gammaproteobacteria, Acidobacteriae, and Anaerolineae appeared as characteristic groups, being particularly abundant in specific sponge samples. Community structures ranged from dominance by one or two abundant taxa to more taxonomically diverse and evenly distributed microbiomes. A notable proportion of sequences were unassignable to known taxa, suggesting the occurrence of previously uncharacterized microbial lineages in these sponges. By combining host species identification with microbiome profiling, this study provides new foundations on the microbial ecology of Korean sponge holobionts, providing higher-resolution taxonomic classification, improved diversity estimates, and enhanced characterization of evolutionary relationships among symbionts. These findings may support future investigations into host–microbe interactions, potential ecological functions, and the management of marine genetic resources. Full article

The oral microbiome of patients with acute lymphoblastic leukemia (ALL) undergoes changes caused by the neoplasia as well as the antimicrobial activity of chemotherapy (CTX), which promotes the development of oral mucositis (OM). This study aimed to analyze the oral microbiome dynamics and salivary cytokine production in pediatric ALL patients before and during CTX, comparing children who did and did not develop OM. We conducted a longitudinal, observational, and analytical study including 32 newly diagnosed pediatric ALL patients (ages 2–16 years) undergoing CTX. Oral rinse and non-stimulated saliva samples were collected at baseline (day 0), day 14, and day 21 of induction of CTX, with an additional sample taken during OM episodes when possible. Microbiome analysis was performed using 16S rRNA sequencing on an Illumina MiSeq platform, and salivary cytokines were measured using a Luminex multiplex assay. The most pronounced microbiome changes occurred on day 14, particularly in patients who developed OM, characterized by higher α diversity, increased abundance of opportunistic taxa, and elevated IL-6 concentrations. In contrast, patients who did not develop OM exhibited a more stable microbial composition. Overall, these findings indicate that temporal oral dysbiosis and increased IL-6 may serve as early markers and potential predictors of OM development during chemotherapy in pediatric ALL patients. Full article

Pseudouridine (Ψ), the most abundant RNA modification, plays essential roles in shaping RNA structure, stability, and translational output. Beyond cancer, Ψ is dynamically regulated across numerous physiological and pathological contexts—including immune activation, metabolic disorders, stress responses, and pregnancy-related conditions such as preeclampsia—where elevated Ψ levels reflect intensified RNA turnover and modification activity. These broad functional roles highlight pseudouridylation as a central regulator of cellular homeostasis. Emerging evidence demonstrates that Ψ dysregulation contributes directly to the development and progression of several women’s cancers, including breast, ovarian, endometrial, and cervical malignancies. Elevated Ψ levels in tissues, blood, and urine correlate with tumor burden, metastatic potential, and therapeutic responsiveness. Aberrant activity of Ψ synthases such as PUS1, PUS7, and the H/ACA ribonucleoprotein component dyskerin alters pseudouridylation patterns across multiple RNA substrates, including rRNA, tRNA, mRNA, snoRNAs, and ncRNAs. These widespread modifications reshape ribosome function, modify transcript stability and translational efficiency, reprogram RNA–protein interactions, and activate oncogenic signaling programs. Advances in high-resolution, site-specific Ψ mapping technologies have further revealed mechanistic links between pseudouridylation and malignant transformation, highlighting how modification of distinct RNA classes contributes to altered cellular identity and tumor progression. Collectively, Ψ and its modifying enzymes represent promising biomarkers and therapeutic targets across women’s cancers, while also serving as sensitive indicators of diverse non-cancer physiological and disease states. Full article

Investigating the prevalence and molecular genetic characteristics of Anaplasma ovis, Theileria spp., Anaplasma phagocytophilum, and hemotropic Mycoplasma infections in sheep populations across different regions of Gansu Province is of significant importance for the prevention and control of these pathogens. A total of 1523 sheep blood samples were collected from 19 counties (districts) in Gansu Province. Pathogen screening was conducted using PCR-based molecular detection techniques, followed by sequencing and phylogenetic analysis of specific genes (e.g., Msp4, 18S rRNA) from selected positive samples. Blood-borne pathogens infections in Gansu Province were widespread but unevenly distributed geographically. Theileria spp. and Anaplasma ovis were the dominant pathogens, with overall infection rates of approximately 16.7% and 9.6%, respectively. The highest Anaplasma ovis infection rate (82.5%) was observed in the Gannan region, where co-infections were common (24/97). An exceptionally high Theileria spp. infection rate (87.5%) was detected in the Zagana area. No pathogens were detected in Wuwei, Jingyuan, Huining, Jingtai, Qinghuan, or Maqu. Phylogenetic analysis revealed that the Msp4 gene sequences of Anaplasma ovis isolates from Gansu shared 99.48% homology with strains from Europe, Asia, and Africa. Anaplasma phagocytophilum isolates also showed high homology (99.53–99.84%) with multiple global strains. Seasonal data indicated significantly higher Theileria spp. infection rates in spring (23–34%) compared to other seasons (approximately 12%). Gansu Province is an endemic area for multiple blood-borne pathogens, with distinct regional clustering and seasonality in prevalence. The high conservation of pathogen gene sequences suggests genetic stability. This study provides essential epidemiological baseline data and a scientific foundation for targeted prevention and control of blood-borne pathogen diseases in sheep in Gansu Province. Full article

Rectifying the microbiome perturbed by Eimeria invasion might alleviate the adverse effects of coccidia on broiler growth. This study employed an in vitro fermentation model to investigate the direct, host-independent effects of two probiotics—Lactobacillus rhamnosus (LR) and Bacillus subtilis (BS)—on the cecal microbiome and metabolome perturbed by Eimeria tenella. Four in vitro fermentation treatments consisted of a healthy control (cecal slurry samples from health broilers), an Eimeria-disturbed control (slurry samples from infected broilers), an LR treatment (Eimeria-infected slurry + 3 × 10⁵ of LR cfu/mL), and a BS treatment (Eimeria-disturbed group + 3 × 10⁵ of BS cfu/mL). 16S rRNA sequencing and metabolomic analysis revealed that Eimeria infection resulted in an increase in microbial alpha diversity, promoted opportunistic pathogens, including Helicobacter and Bacteroides, and suppressed commensals like Lactobacillus, concurrently altering 530 intracellular metabolites. Probiotic supplementation partially restored microbial composition. Notably, LR inoculation rectified 107 metabolites across pathways including galactose metabolism and phosphotransferase systems, primarily affecting membrane phospholipid balance. In contrast, BS addition restored only 64 metabolites, largely related to secondary metabolism. The current in vitro study indicates that LR can directly modulate key metabolic disturbances in a dysbiotic microbiota, while the BS may be more dependent on host-mediated interactions. Full article

The insect gut microbiome contributes to various host physiological processes and behaviors, such as digestion, nutrient absorption, immunity, mate choice, and fecundity. The social environment can shape gut microbial communities. Mixed-sex vs. female-only rearing is an important social context because it differs in exposure to the opposite sex and mating opportunities, which may in turn affect female physiology that may influence their gut microbiome. Despite the growing recognition of these social-microbial interactions, most studies have relied on 16S rRNA amplicon sequencing or qPCR, which provide only coarse taxonomic resolution and limited functional insight. In this study, we used whole-genome shotgun metagenomics to examine changes in microbial diversity and functional gene composition in the female field cricket Teleogryllus occipitalis (Serville) (Orthoptera: Gryllidae) reared under two social conditions: mixed-sex rearing and female-only rearing. Species richness and diversity analyses revealed that community composition separated between females from mixed-sex and female-only rearing. Functional profiling indicated higher relative abundances of genes annotated to nutrient processing and inter-bacterial competition in females from mixed-sex rearing, whereas females from female-only rearing showed relative enrichment of genes annotated to stress resistance and nitrogen fixation. These findings provide a genome-resolved foundation for testing how social rearing conditions covary with gut microbiome composition and functional potential in female crickets. Full article

Antibiotic resistance genes (ARGs) pose a serious threat to the environment worldwide. The guts of soil animals are a hotspot for ARGs and denitrification in soils. However, it is unclear how denitrification affects the spread of ARG in the earthworm’s gut. In this study, the typical soil earthworm Pheretima guillelmi was employed, and was used for performing anoxic incubation with gut content amended with nitrate and nitrite. To analyze the data, a combination of chemical analysis, 16S rRNA-based Illumina sequencing, and high-throughput qPCR were employed. Nitrate treatments, particularly at 5 mM, caused substantial reductions in nitrate concentrations, with a corresponding increase in nitrite, nitrous oxide (N₂O), and nitric oxide (NO) emissions compared to the treatments with the addition of 1 and 2 mM nitrate. Nitrite (0.2, 0.5 and 1 mM) amendments also enhanced the accumulation of nitrogen intermediates. Organic acid production, including acetate and pyruvate, was the highest under the 5 mM nitrate treatment. This treatment also promoted the highest level of glucose utilization, suggesting that glucose metabolism supports enhanced organic acid production. Both nitrate and nitrite treatments exhibited the pronounced enrichment in ARGs, particularly for beta-lactam and multidrug resistance genes. Denitrifying bacteria such as Aeromonas, Bacillus, Raoultella, and Enterobacter were identified as key hosts for these ARGs. These results emphasized that denitrifying bacteria play a pivotal role in the horizontal transfer of ARGs, underscoring the need for careful nitrogen management in agricultural practices to control the spread of antibiotic resistance in natural environments. Full article

This study successfully developed an oral vaccine for Type 1 Diabetes utilizing recombinant Lactococcus lactis expressing the GAD65 autoantigen. We conducted an in-depth investigation into its protective mechanisms in NOD mice, with a particular focus on its effects on the gut microbiota and metabolome. The administration of the GAD65-L. lactis vaccine resulted in a significant delay in diabetes onset and the preservation of pancreatic function. Our analyses revealed notable alterations in the gut microbial ecosystem, enhancing its diversity and the abundance of beneficial bacteria. Metabolomic profiling indicated time-dependent changes in metabolic pathways, with a marked enrichment of pyrimidine metabolism at 16 weeks and arachidonic acid metabolism at 24 weeks after vaccination by both GAD65-L. lactis and NZ9000-L. lactis. Integrated correlation analysis identified specific microbiota–metabolite interactions, including associations between Ruminiclostridium and lipid species in the GAD65-L. lactis group. These modifications in the microbial community and metabolic landscape were accompanied by enhanced immunoregulatory responses in intestinal LPLs, including expanded Treg populations and suppressed CD8⁺ T cells, a rising trend in IL-10-producing naive dendritic cells, and increased concentrations of TGF-β. Full article

The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration. Full article

Retinitis pigmentosa (RP), an inherited retinal disorder, leads to progressive photoreceptor degeneration and irreversible blindness, with limited treatment options available. Emerging evidence implicates microRNAs (miRNAs) in the pathogenesis of retinal disease, yet understanding of their specific roles in RP remains incomplete. In this study, we employed high-throughput RNA sequencing to profile miRNA expression in a rd1 RP mouse model at postnatal day 14. Our analysis revealed 40 upregulated and 27 downregulated miRNAs in rd1 retinas compared to controls. Notably, miR-142a-5p, miR-223-3p, and miR-653-5p were significantly elevated, while miR-25-3p was downregulated. Given miR-142a-5p’s established roles in apoptosis and inflammation, we investigated its contribution to retinal degeneration. Knockdown of miR-142a-5p in rd1 mice improved retinal function and preserved outer nuclear layer thickness, suggesting a protective effect against photoreceptor loss. These findings highlight miR-142a-5p as a key regulator of RP progression and a promising therapeutic target for mitigating vision loss in retinal degenerative diseases. Full article