Search Results (88)

Alheira is a traditionally smoked, fermented, non-ready-to-eat meat sausage produced in the Trás-os-Montes region of Portugal, where lactic acid bacteria (LAB) are major determinants of product safety and quality. This study used whole-genome sequencing to characterize 59 LAB isolates collected from artisanal alheira produced in six municipalities. Eight species belonging to six genera were identified, and average nucleotide identity analysis resolved 24 non-redundant strain groups. Functional annotation revealed broad repertoires of carbohydrate-active enzymes, proteases, lipases, transport systems, and genes associated with tolerance to acid, oxidative, bile, heat, and salt stress. Genotype–phenotype inference was performed with a subset of 22 strain groups represented by unflagged genome assemblies. After false-discovery-rate correction, carbon-metabolism, transport, energy-metabolism, total functional-gene, acid-stress, bile-stress, and total-stress counts were positively associated with total pH decline. A mixed-effects model showed a positive association between standardized total functional-gene count and acidification ($b=0.137\pm 0.059$, $p=0.049$; marginal $R^2=0.266$, conditional $R^2=0.582$), but within–between decomposition indicated that the association was detectable between species rather than within species. Regularized regression, Random Forest, AICc model comparison, and partial least-squares regression converged on carbon metabolism, transport, energy metabolism, and acid- or bile-stress functions as the principal exploratory signals; however, sparse LASSO regression for variable selection was unstable, and prediction of unobserved species was limited. None of the five targeted pathways: acetaldehyde, citrate, diacetyl, exopolysaccharide, and lactose metabolism, remained significant after multiple-testing correction. These findings provide a genomic and phenotypic basis for selecting native starter-culture candidates while emphasizing the need for independent functional and safety validation. Full article

The intrinsic weakness of the budding yeast Saccharomyces cerevisiae in xylose utilization limits its application in biological manufacturing using lignocellulosic biomass. Although the natural yeast strain S. cerevisiae YB-2625 exhibits superior innate xylose-fermenting capability, the underlying mechanisms remain largely unexplored. Here, we employed comparative multi-omics to systematically dissect the molecular basis of its high stress tolerance and superior xylose consumption. Comparative genomics revealed 73,842 single nucleotide polymorphisms (SNPs) and 5191 small insertions/deletions (InDels) in YB-2625 relative to S288C, with significant enrichment in genes associated with chromatin remodeling, transcriptional regulation, and stress signaling. Integration of genomic and transcriptomic data identified candidate variants in key regulators. Functional validation further demonstrated that Tra1, a component of the SAGA, SLIK, and NuA4 histone acetyltransferase complexes, acts as a global regulator with growth-coupled effects on stress tolerance and xylose metabolism. Deletion of TRA1 significantly reduced the final biomass in xylose medium. Moreover, deletion of RTT109 specifically impaired growth on xylose without affecting any of the tested stress tolerance phenotypes. We further examined global chromatin accessibility changes upon deletion of the histone acetyltransferase gene NGG1, a manipulation previously shown to substantially enhance xylose utilization in the engineered YB-2625 background. ATAC-seq analysis revealed that loss of Ngg1 alters chromatin accessibility at loci governing carbohydrate metabolism and stress responses, thereby establishing a direct link between epigenetic remodeling and the superior phenotype of YB-2625. Our findings provide a basis for deciphering the regulatory circuitry governing xylose utilization in recombinant yeast and for the rational engineering of robust strains for lignocellulosic bioconversion. Full article

Cronobacter spp. are opportunistic foodborne pathogens that can cause neonatal meningitis, necrotizing enterocolitis, and sepsis. This study conducted a systematic contamination survey and whole-genome epidemiological analysis of 562 low-water-activity food samples in Hunan Province of China. The results showed an overall Cronobacter spp. detection rate of 41.99% (236/562), with spices exhibiting the highest contamination rate (60.06%), and with high-level contamination samples (>110 MPN/g) concentrated in this category. The 236 isolates comprised 6 species, 120 sequence types, and 39 clonal complexes, with C. sakazakii being the most frequently isolated species (64.83%) and high-risk clones ST4, ST1, ST148, and ST64 prevailing. Multiple virulence genes (TraJ, fur, rcsAB, rpoS) and antimicrobial resistance genes (qnrS1, blaTEM-1, blaCTX-M-55, blaLAP-2, aac(3)-IId, aadA2, tet(A), floR, mcr-9.1, sul2) were detected. Core genome multilocus sequence typing (cgMLST) identified two clustering patterns: Cluster C, whose genetic clustering was consistent with transmission associated with potential common upstream raw materials across different brands and provinces, and Cluster G, whose clustering suggested potential persistent colonization in the production environment across multiple batches of the same brand. This study elucidates the contamination characteristics of Cronobacter spp. in low-water-activity foods from Hunan Province and provides a basis for WGS-based active surveillance and supply chain traceability. Full article

Background/Objectives: Escherichia coli (E. coli) spans commensal, intestinal pathogenic, and extraintestinal pathogenic lineages distributed across human, animal, and environmental reservoirs, yet the extent to which virulence architectures are shared across these compartments remains incompletely understood. Using a One Health framework, we profiled putative virulence determinants in pooled multidrug-resistant (MDR) E. coli source groups representing human, animal, and environmental sectors. Methods: Virulence genes were predicted with VirulenceFinder, and presence–absence profiles were integrated to define functional composition, sector overlap, source-group distribution breadth, and pathotype-associated signatures. Predicted pathogenic potential was assessed with PathogenFinder and compared with pathogenic family richness. Results: Overall, 114 putative virulence genes were detected, with adhesion/colonization functions dominating the virulome (33/114), followed by toxin-associated genes (12/114). A conserved core of 50 virulence genes was shared across all three sectors, including determinants linked to serum resistance (iss, ompT, traT), adhesion (csgA, fimH), stress adaptation (terC), and iron acquisition (sitA, iutA, fyuA). ExPEC-associated determinants were most numerous in environmental source groups (n = 52), whereas diarrheagenic E. coli markers were most frequent in animal-associated groups (n = 42). LEE-associated effectors were infrequent and largely absent from human source groups. Despite ecological differences in virulence composition, pathogenicity scores remained consistently high across sectors (0.83–0.92) and showed no significant association with pathogenic family richness (Spearman’s ρ = 0.197, p = 0.392). Conclusions: Within the limits of pooled source-group analysis, these findings suggest that MDR E. coli across One Health compartments shares a broadly distributed, ExPEC-associated virulence repertoire overlaid with sector-specific pathotype signals, underscoring the value of integrated genomic surveillance while highlighting the need for isolate-resolved analysis. Full article

Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and non-ESBL Escherichia coli across One Health interfaces in Oman. Methods: This prospective cross-sectional study analyzed 295 non-duplicate Escherichia coli isolates derived from 104 clinical, 173 animal [diseased (123) and healthy (50)], 14 sewage and four water sources. Antimicrobial susceptibility testing was performed phenotypically, and a representative subset of 50 ESBL and non-ESBL Escherichia coli from the three interfaces underwent whole genome sequencing to determine MLST, phylogroups, resistance genes, virulence determinants and plasmid replicons. Results: ESBL prevalence was highest in human isolates (73%), followed by sewage (28.6%) and animals (16.3% diseased; 8% healthy). blaCTX-M-15 predominated in humans, whereas blaCTX-M-55 dominated in animals and sewage, suggesting ecological partitioning with partial overlap. Quinolone resistance was lowest in the animal interface. Sewage isolates harbored the most complex resistome, including rmtB and plasmid-mediated quinolone resistance genes. MLST analysis revealed high diversity in human isolates, including globally recognized ExPEC lineages (ST10, ST38, ST73, ST127, ST131), while ST224 dominated in animals with evidence of possible spillover to humans. ST167 was confined to sewage, consistent with environmental maintenance of high-risk clones. Phylogroup structuring showed predominance of A, B2 and D among human isolates and A, B1, and E among animal and sewage isolates. Virulence profiling demonstrated broader virulome diversity in humans, but shared core determinants (fimH, sitA, traT) across all domains. IncFIB(AP001918) was the dominant plasmid replicon, particularly among ESBL isolates, underscoring its role in horizontal gene dissemination. Alarmingly, mutation in pmrB (V161G) was identified in a healthy animal isolate, pointing to a need for greater colistin restriction in animal husbandry. Conclusions: This study highlights plasmid-mediated resistance and shared virulence determinants linking reservoirs; although AMR profile was quite distinct across the three interfaces, human isolates demonstrated greater resistance than animal isolates, suggesting healthcare-driven AMR in Oman. Continued integrated genomic surveillance is essential to monitor gene flow and inform coordinated antimicrobial stewardship strategies. Full article

The rhesus macaque is one of the closest evolutionary relatives to humans, making the study of alternative splicing (AS) during its early embryonic development highly valuable for understanding human embryogenesis and related diseases. However, systematic studies in this context remain limited. Here, a comprehensive bioinformatic analysis of AS was performed using RNA-seq data spanning early rhesus macaque embryogenesis. We identified multiple previously unannotated zygotic genome activation (ZGA) genes, thereby refining the rhesus macaque ZGA gene repertoire. The landscape of AS and differential AS events (DASEs) across early stages was characterized, revealing dynamic and stage-specific regulation, with a marked increase in AS events from the 8-cell to morula stages. In addition, weighted gene co-expression network analysis identified 35 key splicing factors (SFs) involved in regulating early rhesus macaque embryonic development. Finally, we calculated the correlation between differentially expressed SFs and DASEs during the ZGA process, and identified potential regulatory relationships between several SFs (TRA2B, IGF2BP1, HNRNPAB, and MATR3) and specific DASEs. Collectively, this study provides the first systematic analysis of AS dynamics and regulation in early rhesus macaque embryogenesis, highlighting its critical role in development and offering a valuable reference for understanding AS in early human embryos. Full article

Freshwater cladocerans such as Daphnia magna (D. magna) are keystone grazers whose hormone-regulated life history traits make them sensitive sentinels of endocrine-disrupting chemicals (EDCs). The organophosphate flame-retardant tris(2-butoxyethyl) phosphate (TBOEP) and perfluoroethylcyclohexane sulfonate (PFECHS) now co-occur at ng L⁻¹–µg L⁻¹ in surface waters, yet their chronic sub-lethal impacts on invertebrate endocrine networks remain unclear. We analysed two publicly available 21-day microarray datasets (TBOEP: GSE55132; PFECHS: GSE75607) using gene ontology enrichment, STRING protein interaction networks, Drosophila phenotype mapping, and KEGG (Kyoto Encyclopaedia of Genes and Genomes)-anchored frameworks to build putative adverse outcome pathways (AOPs) for D. magna. Differentially expressed genes were clustered into functional modules and hub nodes were ranked by degree and betweenness. TBOEP suppressed moulting and growth, altering 1157 genes enriched for metabolism and membrane processes; hubs VRK1, MIB2, and adenylosuccinate synthetase formed a muscle anatomical development sub-network. PFECHS down-regulated vitellogenin and shifted 879 genes dominated by oxidative-stress and glutathione-metabolism signatures; central nodes UBC9, eIF4A-III, Tra-2α, and HDAC1 linked meiotic-cycle, oogenesis, and cyclic-compound binding. Despite chemical dissimilarity, both compounds converged on Wnt-signalling nodes—TBOEP via presenilin-1, and PFECHS via CK1ε/CK2—thereby reducing TCF/LEF-dependent transcription. Predicted outcomes include impaired oocyte maturation, reduced fecundity, and stunted body size, consistent with observed decreases in length and vitellogenin protein. Our network analysis, based on high-dose, sub-lethal exposures used in the underlying microarray studies, indicates that TBOEP- and PFECHS-induced perturbations can destabilise endocrine, developmental, and metabolic pathways in D. magna without overt lethality, and highlights Wnt-centred key events and hub genes as candidate biomarkers to be evaluated in future low-dose studies that use environmentally realistic exposure scenarios. Hub genes and Wnt-mediated key events emerge as sensitive biomarkers for monitoring mixed EDC exposure. Full article

Light intensity strongly influences the morphological development and photoprotective responses of in vitro plantlets, yet the optimal conditions for hydrangea remain undefined. This study investigated the effects of five light intensity gradients (TrA: 80–120 lux, TrB: 380–480 lux, TrC: 1500–1800 lux, TrD: 3800–4000 lux, TrE: 6000–6400 lux) on Hydrangea macrophylla ‘Qingtian’ plantlets. Plantlets exhibited optimal growth at TrB, showing maximal biomass, leaf expansion, chlorophyll content, and root activity, accompanied by low antioxidant enzyme activities and soluble sugar levels. Nutrient accumulation was greater under low light than under high light conditions. Transcriptome analysis of treatments (TrB and TrE) with marked phenotypic differences revealed 7119 differentially expressed genes (DEGs). Of these, 4582 genes were up-regulated and 2537 were down-regulated. The up-regulated genes were significantly enriched in pathways related to cell walls, the microtubule cytoskeleton, and developmental processes, which are involved in the plant growth and development process, such as photosynthesis, nutrient ion transport and regulation, as well as plant hormone responses and transport; whereas the down-regulated genes were significantly enriched in pathways related to carbohydrate metabolism, oxidoreductase activity, and glutathione metabolism, suggesting that high light stress impairs growth by disrupting carbon and antioxidant processes. These results demonstrated that 380–480 lux is the optimal light intensity for ‘Qingtian’ Hydrangea macrophylla in vitro plantlets. This study provides a foundation for optimizing culture conditions and offers new insights into the molecular regulation of light-responsive genes. Full article

Phalaenopsis orchids are globally significant high-value ornamental flowers due to their strange flower shape, gorgeous color, and long flowering period. The successful implementation of reflowering technology is expected to double the economic value of the Phalaenopsis industry. This study selected the cultivated variety Phalaenopsis ‘Hatuyuki’ as the material to investigate the effects of exogenous gibberellin A₃ (GA₃) application (0, 50, 100, 150, and 200 mg/L) on its reflowering. Growth phenotype analysis indicates that exogenous GA₃ significantly promotes the occurrence of reflowering in Phalaenopsis ‘Hatuyuki’ after the first flowering, specifically manifested in elongated leaves, flower bud differentiation, flower stalk growth, and an earlier onset of flowering. The application of exogenous GA₃ significantly enhances the accumulation of starch, soluble sugars, and proteins in Phalaenopsis ‘Hatuyuki’, while inhibiting the synthesis of free fatty acids. Gibberellins (GA₃, gibberellin A₁ (GA₁), and gibberellin A₈ (GA₈)), cytokinins (6-Benzyladenosine (BAPR) and Kinetin (K)), and indole-3-acetic acids (IAAs) (tryptamine (TRA), indole-3-acetic acid (IAA)) are the core endogenous hormones responding to exogenous GA₃ spraying treatment. Transcriptome analysis identified a total of 3891 differentially expressed genes (DEGs). The KEGG enrichment analysis revealed that the most significantly enriched KEGG pathways included ‘Plant hormone signal transduction’. Key genes involved in the plant hormone signal transduction pathway (AUX, IAA, SAUR, DELLA, MYC2) were validated through qRT-PCR, suggesting that these genes may be crucial for the exogenous GA₃ application that promotes the reflowering of Phalaenopsis ‘Hatuyuki’. Additionally, this study highlights 202 core DEGs responsive to exogenous GA₃. Combined with the analysis of hormone signaling pathways, it provides a new perspective for uncovering the key molecular modules involved in GA₃-regulated reflowering of Phalaenopsis ‘Hatuyuki’. Overall, the findings of this study indicate that exogenous GA₃ application can promote the re-flowering of Phalaenopsis ‘Hatuyuki’. Full article

This study investigated the molecular and phenotypic characteristics of antimicrobial resistance in Escherichia coli isolates recovered from the ceca of healthy broilers in Tunisia. A total of 111 E. coli isolates were obtained from chicken samples collected at slaughterhouses and cultured on cefotaxime-supplemented MacConkey agar. All isolates exhibited a multidrug-resistant (MDR) phenotype, and 72.1% were confirmed as extended-spectrum β-lactamase (ESBL) producers. The most frequent β-lactamase gene was bla_CTX-M-G1, followed by bla_TEM and bla_SHV. Carbapenem resistance genes (bla_OXA-48 and bla_IMP) were detected in 12.6% and 6.3% of isolates, respectively, while six isolates harbored the colistin resistance gene mcr-1. Among the tested virulence genes, fimH, traT, and iutA were the most prevalent, detected in over 70% of isolates. Class 1 integrons were present in 83% of isolates, and class 2 integrons in 39.6%, with gene cassettes encoding resistance to trimethoprim (dfrA) and streptomycin (aadA). These findings highlight the widespread presence of MDR and ESBL-producing E. coli strains with virulence traits and integrons in poultry, underscoring the risk of transmission to humans. This study provides essential data supporting the implementation of integrated surveillance strategies in line with the One Health approach. Full article

Transformer 2 beta (TRA2β) is a critical RNA-binding protein that regulates gene alternative splicing and is involved in cell cycle progression, neuronal differentiation, and cytoskeletal organization. It plays an essential role in embryonic development, particularly neurogenesis, where its deletion leads to severe cortical malformations and perinatal lethality. Dysregulation of TRA2β has been implicated in a range of diseases, including neurological, oncological, and immune-related disorders. Given its broad influence, TRA2β is a compelling candidate for targeted therapies and diagnostic biomarkers. This review highlights recent advances in our understanding of TRA2β regulation and its role in modulating alternative splicing across diverse cell types. It emphasizes TRA2β’s dual function as both a developmental regulator and a disease modulator and explores emerging insights into its therapeutic potential and future research directions. A deeper understanding of the cell-specific regulation of TRA2β may accelerate the development of innovative therapeutic strategies targeting this versatile protein. Full article

Sternal bursitis is an underexplored lesion in poultry, often overlooked in microbiological diagnostics. In this study, we characterized 36 Escherichia coli isolates recovered from sternal bursitis in broiler chickens, combining phenotypic antimicrobial susceptibility testing, PCR-based screening, and whole genome sequencing (WGS). The genetic analysis revealed a diverse population spanning 15 sequence types, including ST155, ST201, and ST58. Resistance to tetracycline and ciprofloxacin was common, and several isolates carried genes encoding β-lactamases, including blaTEM-1B. Chromosomal mutations associated with quinolone and fosfomycin resistance (e.g., gyrA p.S83L, glpT_E448K) were also identified. WGS revealed a high number of virulence-associated genes per isolate (58–96), notably those linked to adhesion (fim, ecp clusters), secretion systems (T6SS), and iron acquisition (ent, fep, fes), suggesting strong pathogenic potential. Many isolates harbored virulence markers typical of ExPEC/APEC, such as iss, ompT, and traT, even in the absence of multidrug resistance. Our findings suggest that E. coli from sternal bursitis may act as reservoirs of resistance and virulence traits relevant to animal and public health. This highlights the need for including such lesions in genomic surveillance programs and reinforces the importance of integrated One Health approaches. Full article

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease affecting motor neurons with a phenotypic and genetic heterogeneity and elusive molecular mechanisms. With the present pilot study, we investigated different genetic mutations (C9orf72, TARDBP, and KIF5A) associated with ALS by generating induced pluripotent stem cells (iPSCs) from peripheral blood of ALS patients and healthy donors. iPSCs showed the typical morphology, expressed stem cell markers both at RNA (OCT4, SOX2, KLF4, and c-Myc) and protein (Oct4, Sox2, SSEA3, and Tra1-60) levels. Moreover, embryoid bodies expressing the three germ-layer markers and neurospheres expressing neural progenitor markers were generated. Importantly, the transcriptomic profiles of iPSCs and neurospheres were analyzed to highlight the differences between ALS patients and healthy controls. Interestingly, the differentially expressed genes (DEGs) shared across all ALS iPSCs are linked to extracellular matrix, highlighting its importance in ALS progression. In contrast, ALS neurospheres displayed widespread deficits in neuronal pathways, although these DEGs were varied among patients, reflecting the disease’s heterogeneity. Overall, we generated iPSC lines from ALS patients with diverse genetic backgrounds offering a tool for unravelling the intricate molecular landscape of ALS, paving the way for identifying key pathways implicated in pathogenesis and the disease’s phenotypic variability. Full article

Background/Objectives: Klebsiella pneumoniae ST307 is emerging as a significant global high-risk antimicrobial-resistant (AMR) clone with a notable capacity to acquire and disseminate resistance genes. However, there is limited research on the pathogenicity, virulence, and adaptation of ST307 strains and on the clinical characteristics of infected patients. Methods: In this study, a carbapenem-resistant K. pneumoniae (CRKP) ST307 strain named U989 was isolated from a urine culture of a hospitalized patient in Volos, Greece, in July 2024. Whole-genome sequencing was performed to identify resistance genes to β-lactams bla_KPC-2, bla_CTX-M-15, bla_TEM-1B, bla_OXA-1, bla_OXA-10, bla_SHV-106, and bla_VEB-1 and resistance genes to other antibiotics. Results: A genomic analysis also revealed the presence of virulence factors such as iutA, clpK1, fyuA, fimH, mrkA, Irp2, and TraT and an IncFiB(pQil)/IncFII(K) replicon, which harbors the bla_KPC-2 gene. Additionally, the transposable element Tn4401 was identified as a key vehicle for the mobilization of the bla_KPC-2 resistance gene. Finally, this is the report of a high-risk CRKP ST307 clone expressing KPC-2, SHV-106, CTX-M-15, and VEB-1 bla genes in Greece. Conclusions: The coexistence of these resistance genes in addition to aminoglycoside, quinolone, and other resistance genes results in difficult-to-treat infections caused by respective carrier strains, often requiring the use of last-resort antibiotics and contributing to the global challenge of antimicrobial resistance. Full article

tet(X4)-positive IncHI1 plasmids are widely prevalent in various bacteria. To understand their transmission characteristics, we analyzed two extensively drug-resistant (XDR) Escherichia coli strains isolated from pet dog feces in Henan Province, China. Strain T28R harbored tet(X4)-positive IncHI1, IncF18:A-:B-, and mcr-1-positive IncI2 plasmids, while T16R carried tet(X4)-positive IncHI1, F16:A-:B-, and mcr-1-positive IncX4 plasmids. Four representative fusion plasmids, pT28R-F1, pT28R-F2, pT28R-F3, and pT16R-F1, in transconjugants were analyzed using WGS and PCR mapping. The results showed that IS26 from the IncF18:A-:B--plasmid attacked the conjugative transfer-associated genes trhc and rsp on the IncHI1 plasmid, generating pT28R-F1 and pT28R-F2. pT28R-F3 was generated through ISCro1- and ISCR2-mediated homologous recombination, deleting the Tra1 region of the IncHI1 plasmid. T16R-F1 emerged from ISCR2- and IS1B-mediated homologous recombination, losing transfer regions of parental plasmids. Notably, fusion plasmids lost the temperature sensitivity of the IncHI1 plasmid, with conjugation frequencies between 1.57 × 10⁻⁴ and 3.84 × 10⁻⁵ at 28 °C and 37 °C. The findings suggest that tet(X4)-positive IncHI1 plasmids could be mobilized with the assistance of conjugative helper plasmids and that fusion events enhance the adaptability of these plasmids, thus facilitating the spread of antibiotic resistance, posing a growing public health threat. Full article