Artificial cells, nanomedicine, and biotechnologyNi Li, Lin Tian, Haiyun Wei
Preeclampsia (PE) is a severe pregnancy-specific complication characterized by new-onset hypertension and proteinuria after 20 weeks of gestation, which can cause multi-organ damage and life-threatening outcomes for both mothers and foetuses. Its pathogenesis remains incompletely elucidated, with placental dysfunction widely recognized as a core pathogenic factor. This study integrated multiple placental transcriptome and single-cell sequencing datasets from the Gene Expression Omnibus (GEO) database, employing a multi-dimensional bioinformatics approach - including differential expression analysis, Weighted Gene Co-expression Network Analysis (WGCNA), machine learning, molecular subtype clustering, single-cell resolution analysis, and intercellular communication analysis - to systematically identify PE-related key genes, construct a diagnostic model, define molecular subtypes, and explore potential molecular mechanisms. Results showed 10 differentially expressed genes (DEGs) were identified in PE placental tissues; WGCNA pinpointed the turquoise module as the core PE-associated module. Further screening using 11 machine learning algorithms identified 9 feature genes with high diagnostic value (DDR1, DIO2, FSTL3, HK2, HTRA4, LEP, SERPINA3, TMEM45A, TREM1). A diagnostic model built with the 'Stepglm[forward]' algorithm exhibited excellent performance in both training and validation sets (average AUC = 0.865). Molecular subtype analysis classified PE samples into two subtypes (C1, C2) with significantly distinct immune infiltration profiles, where the C1 subtype showed higher immune cell infiltration. Single-cell analysis identified 11 cell types in PE placental tissue and highlighted TMEM45A as a key DEG. Intercellular communication analysis revealed the VEGF signalling pathway as the core driver of abnormal cellular crosstalk in PE, primarily mediating signal transduction between villous cytotrophoblast cells (VCT), extravillous trophoblast cells (EVT), and endothelial cells. Hypoxia scoring analysis demonstrated significantly higher hypoxia levels in the PE group compared to normal controls, with TMEM45A expression positively correlated with hypoxia scores. This study provides novel insights into the molecular pathogenesis of PE and offers potential biomarkers and a theoretical basis for its early diagnosis and targeted therapy.
Scandinavian cardiovascular journal : SCJBjørn Edvard Seim, Yusuf Khan, Margrethe Flesvig Holt, Aleksandra Ratajska, Annika Michelsen, Monica Myklebust Ringseth, Runar Lundblad, Bente Halvorsen, Kirst…
Objectives. Thoracic aortic aneurysms (TAAs) are often found in younger individuals and approximately 20% may be associated with heritable thoracic aortic disease (HTAD). There are some data on genomic biomarkers reflecting inflammation and extracellular matrix remodelling in HTAD. However, data that accurately reflect the corresponding protein changes are scarce. Our aim was to quantify proteins by using targeted proteomics in HTAD patients versus healthy controls, to better understand the underlying pathophysiology. Methods. Patients with Loeys-Dietz syndrome (LDS, n = 8), Marfan syndrome (MFS, n = 11), and familial TAA 6, i.e. actin alpha 2 (ACTA2, n = 7) pathogenic variants were recruited at our outpatient clinic. For comparison, blood samples were drawn from 16 healthy controls. Plasma samples were analysed by targeted proteome analysis of 276 proteins using immunoaffinity proteomics. Results. Whereas oncostatin M and pentraxin 3 levels appeared generally higher in HTAD patients, after adjusting for several confounders, significantly higher levels for these markers as well as TNF receptor superfamily member 9 (TNFRSF9), granulysin (GNLY), CD5, vasorin and glycoprotein 1b-α (GP1BA) were only observed in LDS patients compared to healthy controls. Levels of TNFRSF9, GNLY, GP1BA and CD5 correlated positively with Th17 and platelet counts. Conclusions. This discovery study suggests that LDS could represent a particular inflammatory subgroup of HTAD patients potentially reflecting the involvement of Th17 and platelet related mechanisms in the progression of TAA. Larger studies are needed to evaluate if the identified proteins could be used as biomarkers in these patients.
The aging male : the official journal of the International Society for the Study of the Aging MaleMingshun Zuo, Yuanjian Liao, Qiang Xu, Ailing Su, Ni Fu, Chenghong Zou
BACKGROUND: Observational studies link hyperthyroidism to increased prostate cancer (PCa) risk, but causality and mechanisms remain unclear. Graves' disease (GD), the primary cause of hyperthyroidism, involves chronic immune dysregulation that may influence PCa through shared immune pathways. METHODS: We performed bidirectional two-sample Mendelian randomization (MR) using IEU Open GWAS data, then integrated differential expression analysis, weighted gene co-expression network analysis (WGCNA), and machine learning on Gene Expression Omnibus (GEO) datasets to identify shared gene, validated by ROC curves, and analyzed immune profilesusing ssGSEA. RESULTS: MR analysis indicated that genetic predisposition to GD significantly reduced PCa risk (OR = 0.997, 95% CI = 0.996-0.999, p = 0.004), with consistentsensitivity and no reverse causality. Four key genes (BTG2, JUN, JUNB, FOS) were identified as robust shared genes with high predictive accuracy in external validation. Immune profiles analysis revealed disease-specific associations of these genes: BTG2 and JUNB correlated with memory CD8 T cells in GD, whereas all four genes correlated with dendritic cells, mast cells and NK cells in PCa. CONCLUSION: This study provided novel insights into the protective effect of GD against PCa and identified shared genes and immune mechanisms, offering a deeper understanding of the common mechanisms between GD and PCa.
Cell cycle (Georgetown, Tex.)Yunchang Yang, XiangXiang Cao, Nan Feng, Xinyao Kang, Yaofeng Wang, Yunqin Sun
Glioblastoma (GBM) is defined by extreme lethality and transcriptomic plasticity, but the signatures driving the most aggressive tumors remain incompletely defined. In this exploratory in silico study, TCGA-GBM patients were stratified using a strict 1-year overall survival threshold. We integrated differential expression analysis, WGCNA, single-cell RNA-seq, spatial transcriptomics, and virtual knockout simulations. A high-risk signature centered on CCL2 and TIMP1 was identified. Single-cell and spatial mapping linked these genes to an inflammatory, macrophage-enriched microenvironment. The signature inversely correlated with neuronal synapse mimicry scores, suggesting that extreme aggressiveness involves a macroscopic shift from differentiated neuronal states toward an undifferentiated inflammatory phenotype. Virtual perturbation modeling confirmed CCL2 and TIMP1 as highly interconnected network hubs. Despite limitations inherent to computational and retrospective cohorts, our rigorous multi-omics validation identifies the CCL2/TIMP1 axis as a driver of potential prognostic indicator. These findings generate the hypothesis that these mediators reflect a critical inflammatory, mesenchymal-like tumor microenvironment shift, warranting independent cohort validation and experimental investigation.
Gut microbesEmily N Yeo, Ashley W Scadden, Zachary T Caterer, Kristen J Sutton, Iain R Konigsberg, Joanne B Cole, Elizabeth M Litkowski, Zhaoxing Pan, Catherine A Lozupone…
Obesity is a multifactorial condition, and there is wide heterogeneity in responses to weight loss interventions. Although it remains challenging, modeling responses to weight loss interventions can help tailor treatments, increase weight loss success, or improve our understanding of underlying pathophysiology. We leveraged multi-omic (genetics; gut microbiota: taxonomy, inferred gene pathways and metabolite dynamics; blood metabolomics) and clinical data (e.g., lipids, blood glucose) from a 12-month behavioral weight loss trial of adults (n = 150) with overweight/obesity, to forecast longitudinal body mass index (BMI) and BMI change (ΔBMI) using Mixed Effects Random Forests (MERF) and GLMM-Lasso. Across modeling approaches and outcomes, routinely available clinical variables and blood metabolomics consistently improved prediction over basic demographics, and metabolomics added value beyond clinical information. Across models, the combined omic risk score most improved models of longitudinal BMI trajectories, explaining 20.5-26.0% marginal variance (R2m), whereas metabolomic risk scores most improved BMI change prediction (R2m = 52.9-59.3%). Gut microbial taxonomy and inferred gene pathways offered modest but significant gains for some models and outcomes, while metabolite dynamics consistently failed to enhance performance. The most important features in the models included insulin, glycoprotein acetyls, lipoprotein sizes, and certain amino acids, aligning with known inflammatory and metabolic mechanisms. These findings support that select blood-based biomarkers correlate with individual responses to weight loss efforts.
Retinal ischemia-reperfusion injury (RIR) is the main pathogenic mechanisms of acute glaucoma, diabetic retinopathy, central retinal vein occlusion. As a common post-transcriptional modification of eukaryotic RNAs, N6-methyladenosine (m6A) is associated with the pathogenesis of different diseases, including angiogenesis, through the regulation of RNA metabolism and functions. The aim of this study was to identify the potential relevance of m6A RNA methylation in pathogenesis of RIR. A total of 10,851 mRNAs and 23,270 associated m6A methylation modified peaks were identified in the RIR group. Similarly, 10,391 mRNAs and 22,935 associated m6A methylation modified peaks were detected in the Sham group. MeRIP-seq identified 3,871 RIR-specific m6A peaks and 3,624 Sham-specific m6A peaks, in addition to 19,399 shared peaks between groups. Gene ontology (GO) analysis showed that hypermethylated mRNAs were enriched in cellular process, cellular anatomical entity, and binding, while hypomethylated mRNAs were enriched in synaptic signaling, synapse, and gated channel activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that hypermethylated mRNAs were involved in tight junction, hippo signaling pathway, and PI3K-Akt signaling pathway, while hypomethylated mRNAs were involved in Neuroactive ligand-receptor interaction, glutamatergic synapses, cholinergic synapses. Joint analysis identified mRNAs with differential m6A methylation and expression simultaneously. Among them, the expression patterns of Irx4, Kdr, and Lyz2 were confirmed by RT-qPCR to be consistent with the sequencing results. The results revealed an altered m6A epitranscriptome in RIR retinas. These methylated RNAs may act as novel modulators and targets in RIR.
Gut microbesAnna A Bogdanova, Andrea Borbón-García, Ruth E Ley, Alexander V Tyakht
Flagellin, the structural protein of bacterial flagella, activates the innate immune receptor Toll-like receptor 5 (TLR5). However, the ability of different flagellins to bind and stimulate TLR5 varies widely, suggesting that the composition of an individual's flagellin repertoire, defined as flagellome, may influence host-microbiome interactions and inflammation. Here, we developed FlaPro, a computational pipeline for quantification and functional annotation of human gut flagellomes. Functional categories in FlaPro are derived from a machine learning model trained on experimentally characterized flagellins with defined TLR5-binding and stimulatory activities. Application of FlaPro to a multi-omics inflammatory bowel disease (IBD) cohort revealed a marked depletion of flagellome diversity and a reduced ratio of silent to stimulatory flagellins in Crohn's disease and ulcerative colitis. These alterations were consistent across genomic and transcriptional layers, indicating a disease-associated shift toward more stimulatory flagellome profiles. Our findings suggest that specific features of the gut flagellome contribute to TLR5-mediated immune activation and may serve as functionally interpretable microbiome markers for future microbiome-wide association studies in health and disease. The workflow implemented in Snakemake is openly available at https://github.com/leylabmpi/FlaPro.
Artificial cells, nanomedicine, and biotechnologyZhaojun Mei, Xiaoqin Xiong
Kawasaki disease (KD) is a systemic vasculitis in children primarily affecting the coronary arteries, and studies suggest that the gut microbiota may be involved in KD pathogenesis, inflammatory responses, and immune regulation. This study employed an integrative multi-omics strategy to systematically investigate gut microbiota-metabolite interactions in KD. Key molecular targets were identified using network-based analyses and machine learning models, with Mendelian randomization providing causal validation. Single-cell transcriptomics and molecular docking further elucidated immune cell interactions and metabolite-protein binding, highlighting critical regulatory pathways. We identified SELP as a core molecular target in KD, predominantly expressed in platelets and involved in immune and inflammatory responses. Gut microbiota-derived metabolites, including palmitoylethanolamide, pantothenic acid, and 1-O-caffeoylglycerol, may regulate immune cell interactions via the RESISTIN signalling pathway. Altered abundances of microbial taxa such as Bacteroides, Parabacteroides, and Bifidobacterium suggest their potential role in inflammation modulation. Activation of IL-17, TNF, MAPK, and PI3K-Akt pathways further contributes to disease progression, highlighting the microbiota-metabolite-SELP axis as a potential therapeutic target in KD. These findings lay the groundwork for subsequent in vitro and in vivo studies, advancing the development of microbiome-based intervention strategies.
Hematology (Amsterdam, Netherlands)Sufei Kuang, Qixin Liu
BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) presents a complex etiology and challenging diagnosis. This study aims to investigate potential pathogenic genes. METHODS: We identified DLBCL risk genes (DRGs) through expression quantitative trait loci-Mendelian randomization (eQTL-MR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to explore biological functions. Single-cell RNA sequencing (scRNA-seq) data were analyzed to delineate the subcellular localization. Immune infiltration analyses examined the role of genes in the DLBCL immune microenvironment. Finally, drug sensitivity analyses were performed to predict potentially sensitive drugs. RESULTS: Following eQTL-MR and prognostic analyses, we identified 15 genes associated with both the pathogenesis and prognosis of DLBCL. These genes were successfully integrated into a risk gene model, achieving an Area Under the Curve (AUC) of 0.787. GO and KEGG enrichment analyses of genes localized significant pathways, including NF-κB signal transduction. ScRNA-seq analysis suggested that DRGs may be linked to the immune microenvironment of DLBCL. Further immune infiltration analysis confirmed the pivotal role of immune infiltration in the malignant progression of DLBCL. CONCLUSION: This study unveils 15 risk genes as potential pathogenic and therapeutic biomarkers for DLBCL. These findings provide novel insights and targets for understanding the pathogenesis, diagnosis, and treatment of DLBCL.
Human vaccines & immunotherapeuticsTina Zarrinpanah, Maryam Mashhadi Abolghasem Shirazi, Seyed Mohammad Hasan Modarressi, Setareh Haghighat
Vaccines based on purified antigens, recombinant proteins, and nucleic acid platforms increasingly depend on adjuvants to induce robust, durable, and appropriately polarized immune responses in humans. While classical adjuvants such as aluminum salts and oil-in-water emulsions have enabled the success of many licensed vaccines, their largely empirical design limits adaptability to emerging pathogens and population-specific needs. This review presents a translational framework for next-generation vaccine adjuvant development by integrating nanotechnology-based delivery systems, innate immune signaling mechanisms, and systems-level computational strategies relevant to human vaccination. We summarize the mechanisms and clinical relevance of licensed and advanced adjuvants, including alum, MF59, AS01/AS04, saponins, toll-like receptor agonists, and lipid nanoparticles, with emphasis on influenza, HPV, herpes zoster, and COVID-19 vaccines. By linking immunological mechanisms with delivery engineering and predictive modeling, this review highlights rational strategies to support safer and more effective human vaccines.
HLA class I presentation of pathogen-derived peptides is essential for CD8+ T-cell recognition of Toxoplasma gondii. While in vitro MHC ligands have been documented, the in vivo ligandome during infection progression remains poorly characterized. Here, we employed an MS-based immunopeptidomics approach to directly profile the T. gondii immunopeptidome presented by HLA-A *02:01 in transgenic mice. By employing a hierarchical discovery funnel, our analysis identified a comprehensive repertoire of 3,744 unique T. gondii-derived peptides. Subsequent filtering for canonical 8-12mers, matching the typical binding length for HLA-A *02:01 ligands, established a high-confidence foundational ligandome of 3,433 peptides. Source protein analysis revealed that these peptides originate from diverse parasite proteins, including a substantial proportion of previously uncharacterized hypothetical proteins. Notably, specific ligands were consistently detected across both acute and chronic stages, suggesting stable MHC-I presentation throughout the infection cycle. By integrating in silico predictions with experimental validation, we prioritized 73 high-affinity candidates, five of which exhibited robust HLA-A *02:01 binding capacity in vitro and in vivo. Specifically, we identified a novel ligand derived from glycogen synthase (PGS) and determined its co-crystal structure with HLA-A *02:01, revealing favorable binding architecture. Overall, these findings expand the known HLA-A *02:01-restricted ligand landscape of T. gondii and provide a high-priority list of candidates for future functional validation of CD8+ T-cell immunogenicity.
RNA biologyMerin Joy, Alice Cleynen, Nikolay E Shirokikh
RNA modifications have emerged as central regulators of cancer translational control. Unlike transcriptional reprogramming, which unfolds over hours, modification-dependent translational rewiring enables rapid proteomic adaptation to the nutrient-deprived, hypoxic, and immunologically hostile tumour microenvironment. Yet most existing reviews organize epitranscriptomic mechanisms by modification type or cancer hallmark, obscuring the mechanistic logic by which chemical marks collectively reshape the translational apparatus. This review adopts a translation-centric framework, examining how the most abundant modifications on mRNAs, tRNAs, and rRNAs regulate each stage of protein synthesis in malignant cells. We survey the epitranscriptomic toolkit, including modification chemistries, enzymatic writers, readers, and erasers, and detection technologies including nanopore direct RNA sequencing. We then trace how modifications control initiation (m6A-driven mRNA circularization, cap-independent translation via eIF3 and eIF4G2, rRNA 2'-O-methylation-directed cap-to-IRES switching), elongation (m6A-induced ribosome stalling coupled to mRNA decay, tRNA mcm5s2U-mediated codon-biased translation, YTHDF1-dependent elongation factor recruitment), and termination (pseudouridine-mediated stop codon readthrough, NMD evasion). Crucially, we show that mRNA, tRNA, and rRNA modifications do not act in isolation but form integrated networks. For example, mRNA m6A and tRNA mcm5s2U operate on opposing arms of the same regulatory axis, with direct implications for therapeutic design. We assess the expanding drug pipeline, from the METTL3 inhibitor STC-15 now in Phase 1b/2 trials and METTL3-targeting PROTACs to FTO and ADAR1 inhibitors, and argue that biology-informed combination strategies targeting multiple modification axes will be essential for durable clinical responses.
Melioidosis, caused by Burkholderia pseudomallei, is an endemic infectious disease with high mortality in tropical and subtropical regions. Large-scale epidemiological data remain insufficient in China, while comprehensive data integrating genomic epidemiology are rare worldwide. Herein, performed a retrospective analysis of 554 culture-confirmed melioidosis cases in southern China from 2003 to 2022. Genomic characteristics and their relationship with antimicrobial susceptibility and clinical characteristics were analyzed via whole genome sequencing. Core-genome SNP phylogenies were constructed from recombination-masked alignments and compared them with 3,573 publicly available global B. pseudomallei genomes to define their population structure and phylogeographic patterns. Melioidosis predominantly affected male patients (86.8%, 481/554) and those aged 45 -64 years (57.7%). Bacteremia (OR=5.91, p<0.001), diabetes mellitus (OR=2.27, p=0.008), and pulmonary infection (OR=2.26, p=0.005) were identified as risk factors for mortality. Antimicrobial susceptibility testing showed B. pseudomallei exhibited high in vitro susceptibility to imipenem (100%) and ceftazidime (99.6%). Pan-genome analysis confirmed chromosomal functional compartmentalization of the bipartite genome, and genome-wide association study identified high-confidence genetic markers (OR >3 or <0.33) significantly associated with mortality and bacteremia. Furthermore, global phylogenomic analysis identified 10 evolutionary clusters; Chinese isolates were significantly enriched in Cluster 1, a clade shared with Thai strains, and were phylogenetically distinct from Cluster 5, as predominantly composed of Australian isolates. In summary, this large-scale genomic and clinical analysis provides the most comprehensive overview of melioidosis in southern China. The genomic analysis highlighted substantial regional and global genetic diversity, and phylogeographic structuring of B. pseudomallei, underscoring the importance of continued genomic surveillance.
Gut microbesTroels Holger Vaaben, Ditte Olsen Lützhøft, Karl Alex Hedin, Linda Ahonen, Ruben Vazquez-Uribe, Morten Otto Alexander Sommer
The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.
Cercarial dermatitis is an important occupational health problem among rice farmers in Assam and other parts of India. We surveyed 1657 paddy farmers from sixteen villages across four districts of Assam, Northeast India, to determine the prevalence of cercarial dermatitis. Of these, 555 (33.5%) reported dermatitis during the preceding three months, and a subset of affected farmers from Barpeta district showed a high proportion of moderate-to-severe disease, often complicated by secondary bacterial infection. Snail surveys were conducted in thirteen villages across eight districts. Examination of 13,309 freshwater snails representing six species identified Indoplanorbis exustus as the only intermediate host shedding Schistosome cercariae, with an infection prevalence of 6.3% among I. exustus. Experimental infections in mice yielded adult worms that were used for morphological, molecular, immunological, and proteomic studies. Molecular identification based on partial 28S rDNA sequencing confirmed the Assamese isolates as Schistosoma spindale, and phylogenetic analysis placed them firmly within the S. spindale clade together with reference sequences from Nepal and Sri Lanka. SDS-PAGE and immunoblotting identified four dominant immunoreactive antigens of approximately 25, 38, 60, and 100 kDa. Two-dimensional PAGE coupled with MALDI-TOF/TOF MS identified several conserved proteins, including paramyosin, tropomyosin, actin, and heat shock protein 70, based on best database matches. ELISA developed using adult worm antigen showed high diagnostic performance (96% sensitivity and 100% specificity) and outperformed the cercarial antigen-based ELISA. This integrated epidemiological, malacological, molecular, proteomic, and immunological investigation provides comprehensive insight into S. spindale the causative agent of cercarial dermatitis in Assam. The findings highlight the need to recognize cercarial dermatitis as a neglected occupational and zoonotic disease within a One Health framework.
Tuberculosis (TB) remains a significant public health threat in urbanizing regions of China, where shifting population dynamics and migration may amplify TB transmission. We conducted a nine-year prospective epidemiological study of culture-positive TB patients diagnosed in Shenzhen, between 1 January 2014 and 31 December 2022, and employed whole-genome sequencing analysis to describe local transmission of Mycobacterium tuberculosis (Mtb). Mtb transmission hotspots were identified using a non-parametric distance-based mapping approach. We applied a spatially structured logistic regression and hierarchical Bayesian pairwise regression analysis to identify demographic, pathogen, and spatial factors associated with local transmission. A Bayesian phylogenetic analysis was used to infer probable transmission events. Among 4,560 individuals with culture-positive TB, 93.4% (4,261) were internal migrants in China. 21.8% (996/4,560) of individuals had Mtb isolates that belonged to genomic clusters, with multiple transmission foci detected in the central business district and suburban industrial areas. Transmission was more likely to occur among patients of similar age, close geographic proximity, and migrants with a shared provincial origin. Mtb isolates from communities with higher proportions of migrants had an increased risk of clustering. In this rapidly growing urban setting, a significant proportion of cases were documented to arise as a result of local transmission, which appears to be driven by specific social and geographical factors, particularly within migrant populations. Control strategies should therefore move beyond static models toward dynamic interventions that specifically target social networks, high-risk communities, and urban hotspots in dynamic urban environments.
Bacillus cereus is a major foodborne pathogen characterized by robust biofilm formation and increasing antimicrobial resistance. This study identified 2-Methoxycinnamaldehyde (MCA) from Toona sinensis as the principal antibacterial compound and evaluated its inhibitory mechanisms and preservation potential. MCA exhibited potent activity against B. cereus ATCC 11778 (MIC = 150 μg/mL; MBC = 200 μg/mL) and resistant strains. In vitro assays demonstrated that MCA induced concentration-dependent membrane disruption, DNA damage, and intracellular protein leakage. Furthermore, treatment at 1 MIC and 2 MIC significantly impeded biofilm maturation; the secretion of extracellular proteins was reduced by 45.3% and 54.5%, polysaccharides by approximately 93%, and extracellular DNA (eDNA) by over 99%. Correspondingly, biofilm metabolic activity declined by 85.9% and 90.3%, and initial cellular adhesion was reduced by up to 88.1%. Untargeted metabolomic analysis revealed that these phenotypic defects stem from profound disturbances in amino acid biosynthesis, the TCA cycle, and nucleotide metabolism. Molecular docking revealed that MCA targets multiple essential bacterial enzymes, including ribonucleotide reductase, lysyl-tRNA synthetase, pyruvate kinase, betaine aldehyde dehydrogenase, and 5'-nucleotidase, through stable hydrogen bonding and π-interactions. In a refrigerated pork model, MCA completely eliminated B. cereus by day 7 while significantly delaying pH increases and color deterioration. These findings provide the first evidence for MCA as an antibacterial and antibiofilm agent against B. cereus, highlighting its potential in food preservation.
Food microbiologyWen Si Hu, So Hyeon An, Dong Woo Kim, Hyeong Uk Im, Seung Hun Lee, Yu Bao Li, Zi Xuan Liu, Zhi Wei Wang, A Ram Lee, Ui In Kim, Hyeon Ji Je, Yeon Ju Seo, Jin Sa…
Listeria monocytogenes is a gram-positive and facultatively anaerobic foodborne pathogen causing listeriosis. The detection of L. monocytogenes in enoki mushrooms sourced from South Korea and China is particularly critical, given their confirmed implication in recent serious listeriosis outbreaks across the global food supply chain. This study investigates the prevalence, genetic diversity, and phenotypical characteristics of L. monocytogenes in enoki mushrooms from South Korea and China. Out of 129 samples, 24 (18.6%) tested positive, with contamination rates of 17.5% in Korean mushrooms and 19.7% in Chinese mushrooms. Whole-genome sequencing, cgMLST, and pan-genome analyses resolved lineage and sequence-type distributions, revealing predominant serogroup 1/2a (83.3%) and lineage II (90.9%). The pan-genomic assessment of L. monocytogenes strains originating from diverse geographical locations indicated the presence of open genomes, which establishes a strong genetic underpinning for adaptation to varied environments. These strains carrying a multitude of virulence genes that significantly contribute to their heightened pathogenic potential. The phylogenetic tree further demonstrated that these highly related Korean and Chinese isolates were intricately intermingled with outbreak-related strains from the USA, Canada, and Europe, confirming a minimal core-genome genetic distance across the global supply chain. This highly homogenous clone, which was ultimately traced back to enoki mushrooms in South Korea and China, suggests that the globalization of the food trade is the primary driver of its rapid, international dissemination.
Brown milk beverages have garnered widespread attention due to their unique flavor and potential as a functional matrix for probiotic delivery. This study aimed to identify Lacticaseibacillus paracasei strains suitable for fermenting brown milk beverages by combining artificial intelligence-driven predictive screening with experimental validation and metabolomic analysis. Using the iProbiotics platform, 27 L. paracasei strains underwent initial screening, yielding seven candidates for further evaluation. These trains were systematically evaluated for gastrointestinal tolerance and bile salt tolerance, fermentation performance, storage stability, and metabolic profiles. Strains PC724 and PC646 demonstrated superior probiotic and technological properties, outperforming the commercial control strain LC-01 in acidification capacity, viable cell counts, and textural attributes. Over 35 days of refrigerated storage, both strains maintained high viability (>108 CFU/mL) and stable metabolic activity, confirming remarkable storage stability. Non-targeted metabolomics revealed sustained enrichment of carbohydrate metabolism, amino acid metabolism, and global metabolic regulation in PC724 and PC646. These metabolic signatures likely underpin their robust stress tolerance long-term survival. Collectively, integrating artificial intelligence prediction with metabolomic profiling provides a scalable strategy for identifying industrially viable probiotic candidates, offering a valuable framework for developing functional fermented milk beverages.
Food microbiologyAhmed Elsheshtawy, Benjamin G J Clokie, Sasha Saugh, Karen D Adler, Slawomir M Michniewski, Simon MacKenzie, Martha R J Clokie, Thomas Sicheritz-Pontén, Amaya …
The Norway lobster (Nephrops norvegicus) is a high-value seafood product with limited shelf-life under chilled storage. This study investigated microbial succession and spoilage dynamics during ice storage (0 °C, 16 days) using an integrated multi-omics approach combining sensory assessment (Quality Index Method), physicochemical indicators (muscle pH and K-value), culture-dependent microbiology, absolute bacterial load quantification (16S rRNA qPCR), 16S rRNA gene amplicon sequencing and shotgun metagenomics. Quality deterioration was characterised by progressive increases in sensory scores, nucleotide degradation and muscle pH, with rejection occurring at day 7. This transition coincided with a marked increase in bacterial load following an initial lag phase (days 0-5), indicating a critical shift in spoilage progression. Amplicon sequencing revealed a transition from a diverse early community (days 0-3) to a Proteobacteria-dominated assemblage from day 5 onwards, driven by increases in Moritella, Pseudoalteromonas and Aliivibrio. Metagenomic analysis further resolved these dynamics at species-level resolution and identified a limited number of dominant taxa associated with mid-to late-stage spoilage. The convergence of sensory rejection, physicochemical changes and microbial restructuring identifies a mid-storage tipping point in spoilage development. By integrating multi-omics with established quality indicators, this study links microbial succession to measurable spoilage outcomes. The dominant taxa are consistent with known spoilage-associated activities, including proteolysis and off-odour production, while highlighting Moritella as a potential contributor in crustacean spoilage. These findings provide a temporal framework for spoilage progression in N. norvegicus and inform targeted strategies for shelf-life management.