PubMed

Plants (Basel). 2025 Feb 19;14(4):629. doi: 10.3390/plants14040629.ABSTRACTCereal crops are important staple foods, and their defense metabolites hold significant research importance. In this study, we employed LC-MS-based untargeted and widely-targeted metabolomics to profile the leaf metabolome of nine cereal species, including rice, wheat, maize, barley, sorghum, common oat, foxtail millet, broomcorn millet, and adlay. A total of 9869 features were detected, among them, 1131 were annotated, encompassing 18 classes such as flavonoids, lipids, and alkaloids. Results revealed that 531 metabolites were detected in all species, while each cereal crop possessed 4 to 12 unique metabolites. Focusing on defense metabolites, we identified eight benzoxazinoids uniquely present in maize, wheat, and adlay. Hierarchical clustering based on metabolite abundance divided all metabolites into nine clusters, and subsequent pathway enrichment analysis revealed that the stress-related flavonoid biosynthesis pathway was enriched in multiple clusters. Further analysis showed that four downstream compounds of HBOA (2-hydroxy-1,4-benzoxazin-3-one) in the benzoxazinoid biosynthesis pathway were enriched in maize. Wheat uniquely accumulated the 4'-methylated product of tricin, trimethoxytricetin, whereas adlay accumulated the tricin precursor tricetin in the flavonoid biosynthesis pathway. In summary, this study elucidates the metabolic diversity in defense metabolites among various cereal crops, providing valuable background information for the improvement of stress resistance in cereal crops.PMID:40006888 | DOI:10.3390/plants14040629

Plants (Basel). 2025 Feb 19;14(4):625. doi: 10.3390/plants14040625.ABSTRACTFlavonoids are secondary metabolites that are beneficial to life activities and are mainly concentrated in buds and leaves in the form of glycosides. Flavonoid glycosides have important effects on the properties and quality of tea plants. Research has shown that the abundance of flavonoid glycosides varies greatly among different cultivars, but research on the regulatory mechanisms that cause their differential accumulation among tea plant cultivars with different leaf colors is lacking. In this study, an integrated analysis of metabolomics and transcriptomics was conducted to determine the regulatory networks regulating astringency and color-related flavonoids in tea plant cultivars with diverse leaf colors. A total of five anthocyanidins, four catechins, and nine flavonol glycosides were found to partially contribute to the differences in taste and leaf color among tea plant cultivars with diverse leaf colors. Furthermore, 15 MYB genes and 5 Dof genes were identified as potential regulators controlling the expression of eight key structural genes, resulting in differences in the accumulation of specific compounds, including epicatechin (EC), catechin (C), cyanidin, cyanidin 3-O-glucoside, pelargonidin 3-O-glucoside, and quercetin 3-O-glucoside, in tea plant cultivars with diverse leaf colors. These findings provide insights into the development and utilization of resources from tea plants with diverse leaf colors.PMID:40006884 | DOI:10.3390/plants14040625

Plants (Basel). 2025 Feb 18;14(4):613. doi: 10.3390/plants14040613.ABSTRACTCamellia oleifera is a unique woody edible oil tree species in China, and the ovule development affects the yield of seeds. This study selected three different types of C. oleifera clones and used LC-MS, RNA-seq, and other techniques to compare the endogenous hormone contents, gene expression levels, and metabolite changes between normal and aborted ovules. The results showed that high levels of ABA, JA, and SA may lead to the phenotype of ovule abortion. A total of 270 differential metabolites were identified in the metabolome, with L-methionine, citrulline, L-tryptophan, L-phenylalanine, and indolepyruvate being downregulated to varying degrees in the aborted ovules. Genes involved in plant hormone synthesis and response, such as GH3.1, IAA14, PIN1, AUX22, ARF1_2, BZR1_2, GA2ox, ERFC3, ABF2, and PYL8, responded to ovule development. This study elucidates the physiological, metabolic, and transcriptional responses to ovule abortion, providing a theoretical basis for understanding ovule development and yield regulation in C. oleifera.PMID:40006872 | DOI:10.3390/plants14040613

Plants (Basel). 2025 Feb 12;14(4):560. doi: 10.3390/plants14040560.ABSTRACTCallus browning is a significant problem that hinders plant tissue regeneration in Paeonia ostii "Fengdan" by causing cell death and inhibiting growth. However, the molecular mechanism underlying callus browning in P. ostii remains unclear. In this study, we investigated the metabolites and potential regulatory genes involved in callus browning of P. ostii using metabolomic and transcriptomic analyses. We found a significant accumulation of phenolic compounds in the browned callus, represented by flavonoid compounds. Notably, the accumulations of luteotin and disomentin were higher in browning calli compared to non-browning calli. Transcriptomic analysis identified that candidate genes associated with flavonoid biosynthesis, including flavonoid 3-hydroxylase (PoF3H) and flavone synthase II (PoFNSII), were highly expressed in the browned callus of P. ostii "Fengdan". Weighted gene co-expression network analysis (WGCNA) further highlighted that polyphenol oxidase (PoPPO) which encoded polyphenol oxidase, together with flavonoid biosynthesis-related genes such as flavanone 3-hydroxylase (PoF3H) and flavonone Synthase II (PoFNSII), as well as cellular totipotency-related genes wuschel-related homeobox 4 (PoWOX4), were involved in callus browning. Based on these findings, we proposed the molecular mechanism by which flavonoid accumulation, polyphenol oxidation, and cellular totipotency pathways contribute to callus browning in P. ostii. Our study provides new insights into the molecular mechanism underlying callus browning and offers the foundations to facilitate the establishment of an efficient plant tissue regeneration system in P. ostii.PMID:40006819 | DOI:10.3390/plants14040560

Plants (Basel). 2025 Feb 12;14(4):558. doi: 10.3390/plants14040558.ABSTRACTThe color of Zanthoxylum bungeanum Maxim. (Z. bungeanum) is a key quality indicator and a factor limiting the development of its industry. However, the underlying mechanisms governing color formation remain largely unexplored. In this study, an integrative analysis of transcriptome and metabolome profiles was conducted across four developmental stages to elucidate the color formation mechanism in Z. bungeanum. A total of 137 flavonoids were identified as the fruits ripened, with high levels of differentially accumulated metabolites (DAMs), including tricetin and (-)-epigallocatechin, which were strongly associated with color formation. This suggests their significant contribution to the pigmentation process. Nine differentially expressed genes (DEGs) were identified as candidate genes involved in color development. Additionally, 15 transcription factors (TFs) (12 MYB and 3 bHLH) exhibited expression patterns similar to those of structural genes in the flavonoid biosynthetic pathway, indicating their role in regulating flavonoid synthesis. The bioinformatics analysis of three key flavonoid synthesis genes-ZbCHI, ZbFLS, and ZbANR-revealed that all three proteins exhibit hydrophobic structures without transmembrane domains. Among them, ZbANR possesses signal peptide regions, whereas ZbCHI and ZbFLS do not. Subcellular localization predictions suggest that ZbCHI is most likely localized in the chloroplast, ZbFLS in the cytoplasm, and ZbANR in the membrane. Functional analyses revealed that their transient expression in Nicotiana benthamiana (N. benthamiana) increased the flavonoid content, with ZbANR overexpression producing a distinct white phenotype in the plants. This study enriches transcriptomic data and provides a comprehensive understanding of flavonoid metabolism and the molecular basis of color formation in Z. bungeanum, offering a valuable theoretical foundation for future breeding programs.PMID:40006817 | DOI:10.3390/plants14040558

Plants (Basel). 2025 Feb 11;14(4):557. doi: 10.3390/plants14040557.ABSTRACTCeratonia siliqua L. (Fabaceae) is an evergreen sclerophyllous species that successfully overcomes the challenges of the Mediterranean climate. Commonly, biosynthesis of secondary metabolites is a major reaction of the plants thriving in the Mediterranean formations against temperature stress. Due to concerns about the climate crisis, we studied the impact of 6-day low (5 °C) and high (40 °C) temperature stress on young carob seedlings. In stressed plants, mainly the heat-treated, the leaves appear xeromorphic. Parameters of the physiology of the plants such as chlorophyll-a and -b, total phenolic content, and oxidative stress were measured and presented via Principal Component Analysis. Chlorophyll-a and -b contents are inferior in cold-stressed leaves while heat-stressed leaves accumulate more phenolics and experience higher oxidative stress as compared to their cold-stressed counterparts. The phytochemical profile of different extracts obtained from stressed carob leaves was identified so as to gain insight into metabolites produced under stress. Moreover, LC-HRMS/MS metabolomic workflow was utilized for the discovery of biomarkers, over- or under-regulated in stressed conditions. The antimicrobial activity of carob leaf extract fractions was assessed against six human pathogen strains and three phytopathogen bacterial strains. MeOH-H2O and dichloromethane (DCM) extracts presented notable activity against Candida albicans and Saccharomyces cerevisiae, while DCM extracts inhibited the growth of Erwinia amylovora. We may conclude that carob tree exposure to temperature stress does not have a significant influence on secondary metabolic pathways.PMID:40006816 | DOI:10.3390/plants14040557

Plants (Basel). 2025 Feb 11;14(4):549. doi: 10.3390/plants14040549.ABSTRACTAlthough the mechanisms underlying albino phenotypes have been examined in model plants and major crops, our knowledge of bract albinism is still in its infancy. Davidia involucrata, a relic plant called dove tree, is best known for the intriguing trait with a pair of white bracts covering the capitula. Here, comparative physiological, cytological, proteomic, and metabolomic analyses were performed to dissect the albinism mechanism of D. involucrata bracts. The bracts exhibited low chlorophyll and carotenoid contents, reduced photosynthetic efficiency, and impaired chloroplast structure. The severe deficiency of photosynthetic pigments and the substantial decrease in cuticle thickness made the bracts light-sensitive. In total, 1134 differentially expressed proteins (DEPs) were obtained between bracts and leaves. Pathway enrichment analysis of DEPs revealed that photosynthetic pigment biosynthesis and photosynthesis were suppressed, whereas protein processing in endoplasmic reticulum, flavonoid biosynthesis, and the ubiquitin-proteasome system (UPS) were activated in bracts. Strikingly, DEPs implicated in chloroplast development, including PPR and AARS proteins, were mainly down-regulated in bracts. We further investigated albinism-induced metabolic changes and detected 412 differentially abundant metabolites (DAMs). Among them, enhanced flavonoids accumulation can plausibly explain the role of bracts in pollinator attraction. Amino acids and their derivatives in bracts showed remarkably increased abundance, which might be causally linked to enhanced UPS function. Our work could lay foundations for understanding albinism mechanisms and adaptive significance of plant bracts and facilitate future utilization of D. involucrata resources.PMID:40006808 | DOI:10.3390/plants14040549

Plants (Basel). 2025 Feb 10;14(4):538. doi: 10.3390/plants14040538.ABSTRACTAlthough metabolomics is widely used to assess the detrimental effects of antibiotics and characterize stress response, the relationships between metabolites and biological endpoints following antibiotics remain unknown. In our study, we exposed ryegrass seeds to sulfamethoxazole for five days. The results showed that sulfamethoxazole inhibited plant growth (by 12.90-85.83%). It also decreased chlorophyll content (by 35.40-93.32%), carotenoid content (by 32.76-90.18%), and root cell permeability (by 98.43-99.29%), but increased root reactive oxygen species (ROS) concentration (increasing rate: 11.32- to 137.36-times). Moreover, high sulfamethoxazole concentrations increased superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. To elucidate the association between metabolites and biological endpoints, we conducted an orthogonal partial least squares analysis. The results showed that sulfamethoxazole significantly altered six metabolic pathways. Among the metabolites modulated by sulfamethoxazole, amino acids mainly affected root growth and ROS concentration, whereas carbohydrates were substantially associated with the effect of sulfamethoxazole on cell permeability. Many metabolites had contrasting effects. For example, some metabolites increased root fresh weight and improved cell permeability by decreasing ROS levels and SOD, POD, and CAT activities. By contrast, some metabolites negatively affected root fresh weight and cell permeability by increasing ROS levels and SOD, POD, and CAT activities. These observations bring new insights into ryegrass responses to sulfamethoxazole-induced stress.PMID:40006797 | DOI:10.3390/plants14040538

Plants (Basel). 2025 Feb 9;14(4):531. doi: 10.3390/plants14040531.ABSTRACTResurrection plants employ unique metabolic mechanisms to protect themselves against damage caused by desiccation. This study aimed to identify metabolites, using gas chromatography-mass spectrometry, which were differentially abundant in Eragrostis nindensis at different stages of dehydration and rehydration in leaves which are destined to senesce on desiccation termed "senescent tissue" (ST) and those which remain desiccation-tolerant during water deficit and are termed "non-senescent tissue" (NST). Furthermore, the study compared the shoot and root systems during extreme water deficit and recovery therefrom to unravel similarities and differences at the whole plant level in overcoming desiccation. Shoot metabolomics data showed differentially abundant metabolites in NST, including raffinose, sucrose, glutamic acid, aspartic acid, proline, alpha-ketoglutaric acid, and allantoin, which act as major drivers for plant desiccation tolerance and aid the plant post-rehydration. The metabolites which accumulated in the ST-indicated initiation of programmed cell death (PCD) leading to senescence. The roots accumulated fewer metabolites than the shoots, some exclusive to the root tissues with functions such as osmoprotection, reactive oxygen species quenching, and signaling, and thus proposed to minimize damage in leaf tissues during dehydration and desiccation. Collectively, this work gives further insight into the whole plant responses of E. nindensis to extreme dehydration conditions and could serve as a model for future improvements of drought sensitive crops.PMID:40006790 | DOI:10.3390/plants14040531

Vet Sci. 2025 Feb 8;12(2):147. doi: 10.3390/vetsci12020147.ABSTRACTPorcine Reproductive and Respiratory Syndrome (PRRS) is a contagious disease that impacts swine health worldwide. Lipid metabolism plays a vital role in energy production and is regulated by various genes involved in lipogenesis and lipolysis. In this study, we found that PRRSV infection significantly reduced the protein expression of STEAP3. The overexpression of STEAP3 can notably inhibit PRRSV replication. Additionally, we utilized transcriptomics and metabolomics to examine the effects of STEAP3 on PRRSV replication, identifying important pathways associated with energy metabolism and lipogenesis. We subsequently found that STEAP3 can suppress PRRSV replication by regulating fatty acid synthesis and enhancing lipid droplet formation. Overall, these findings indicate that STEAP3 could be a potential target for developing strategies to manage PRRSV infection by modulating lipid metabolism.PMID:40005907 | DOI:10.3390/vetsci12020147

Vet Sci. 2025 Feb 7;12(2):138. doi: 10.3390/vetsci12020138.ABSTRACTViruses can manipulate the host metabolism to achieve optimal replication conditions, and central carbon metabolism (CCM) pathways are often crucial in determining viral infections. Feline calicivirus (FCV), a diminutive RNA viral agent, induces upper respiratory tract infections in feline hosts, with highly pathogenic strains capable of precipitating systemic infections and subsequent host cell necrosis, thereby presenting a formidable challenge to feline survival and protection. However, the relationship between FCV and host cell central carbon metabolism (CCM) remains unclear, and the precise pathogenic mechanisms of FCV are yet to be elucidated. Upon FCV infection of Crandell-Rees Feline Kidney (CRFK) cells, an enhanced cellular uptake of glucose and glutamine was observed. Metabolomics analyses disclosed pronounced alterations in the central carbon metabolism of the infected cells. FCV infection was found to augment glycolytic activity while sustaining the tricarboxylic acid (TCA) cycle flux, with cellular ATP levels remaining invariant. Concurrently, both glutamine metabolism and the flux of the pentose phosphate pathway (PPP) were noted to be intensified. The application of various inhibitory agents targeting glycolysis, glutamine metabolism, and the PPP resulted in a significant suppression of FCV proliferation. Experiments involving glucose and glutamine deprivation demonstrated that the absence of either nutrient markedly curtailed FCV replication. Collectively, these findings suggest a critical interplay between central carbon metabolism and FCV proliferation. FCV infection stimulates CRFK cells to augment glucose and glutamine uptake, thereby supplying the necessary metabolic substrates and energy for viral replication. During the infection, glutamine emerges as the primary energy substrate, ensuring ATP production and energy homeostasis, while glucose is predominantly channeled into the pentose phosphate pathway to facilitate nucleotide synthesis.PMID:40005898 | DOI:10.3390/vetsci12020138

Vet Sci. 2025 Feb 1;12(2):102. doi: 10.3390/vetsci12020102.ABSTRACTThis study aimed to investigate the changes in fecal short-chain fatty acids (SCFAs) content in UCP1 knock-in pigs (KI pigs) and their effect on adipogenesis. Fecal samples from five 6-month-old wild-type (WT) and KI pigs were collected for targeted metabolomics and 16s rRNA sequencing analyses to identify differences in SCFAs and gut microbiota that may contribute to regulating fat deposition in pigs. The metabolome of pig fecal samples targeted for an analysis of SCFAs identified seven SCFAs, with caproic acid (except isovaleric acid) being the significantly different one. The results of the fecal 16s rRNA analysis demonstrated a notable reduction in the abundance of Streptococcus spp. in the KI pigs in comparison to the WT pigs, with a statistically significant difference. Correlation analyses demonstrated a statistically significant positive correlation between the abundance of Streptococcus spp. and SCFAs, as well as pig body weight and fatness. It was postulated that the reduction in SCFAs in the intestinal tracts of KI pigs may be associated with a reduction in Streptococcus spp. abundance. Compared to WT pigs, the concentration of fecal SCFAs in KI pigs was significantly reduced, which may be related to the decreased abundance of Streptococcus. The in vitro experiments showed that caproic acid could significantly enhance the differentiation efficiency of porcine SVF cells into mature adipocytes by activating the FFAR4 gene.PMID:40005862 | DOI:10.3390/vetsci12020102

Vet Sci. 2025 Jan 22;12(2):79. doi: 10.3390/vetsci12020079.ABSTRACTIn lactating ewes, energy demand increases for milk production, reserve mobilizations, and body weight maintenance. For reconversion to energy, ruminants require ruminal propionate production because it is the most predominant substrate for gluconeogenesis and one of the most relevant pathways since it allows an adequate supply of glucose. Calcium propionate supplementation is an alternative to increase glucose production by an external additive. Thus, the objective was to evaluate the effect of calcium propionate (CaPr) on milk production and milk metabolomic profile on lactating ewes. Sixteen Rambouillet (65.3 ± 6.2 kg BW; three years old) were randomly assigned one of two experimental treatments: (a) basal diet without supplementation (CP/0S) and (b) basal diet + 30 g d-1 of CaPr (CP/30S). The experimental period was from parturition day until day 60 (baby lamb weaning). A completely randomized design was used and analyzed with a mixed model. Initial and final lactating weight and milk production differed statistically (p < 0.05) between treatments. CP/30S led to differential changes (p < 0.05) in the lactation curve, showing significant milk production over eight-week measurements. Lactation peak (mL), maximum production (mL), and lactational persistency (d) were superior (p < 0.05) for supplemented ewes. An 11.4% variability was shown in a principal component analysis between treatments. For CP/0S, 63 bioactive compounds were detected, and 55 for CP/30S treatment. The metabolites detected in CP/0S showed that only fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, and fatty acid elongation pathways were affected (p < 0.05) in milk. However, for CP/30S, metabolic pathways related (p < 0.05) were fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, fatty acid elongation, phenylalanine metabolism, and steroid metabolism in milk samples. Calcium propionate supplementation increases milk performance and lactation persistency-induced changes in specific metabolic milk production pathways.PMID:40005839 | DOI:10.3390/vetsci12020079

Microorganisms. 2025 Feb 19;13(2):459. doi: 10.3390/microorganisms13020459.ABSTRACTGlobal climate change has accelerated the reduction of permafrost regions across different altitude gradients, shortening the duration of the freezing period to varying extents. However, the response of the soil microorganisms of frozen soils along altitude gradients remains unclear. In this study, we employed 16S rRNA sequencing and LC-MS metabolomics to investigate the response of soil microbial communities and soil metabolites to vertical stratification in the permafrost soils of the Qinghai Lake region. The results indicated that Proteobacteria, Firmicutes, and Actinobacteria were key soil bacterial phyla in the permafrost soils of Qinghai Lake during the freezing period, with Proteobacteria and Firmicutes showing significant sensitivity to vertical stratification (p < 0.05). The majority of the physicochemical factors exhibited a trend of initially increasing and then decreasing with increasing altitude, whereas pH showed the opposite trend. pH and moisture content were identified as the most important environmental factors influencing soil bacterial community structure. Deterministic processes dominated the assembly of bacterial communities of frozen soils in the Qinghai Lake basin. Co-occurrence network analysis showed that increasing altitude gradients led to a higher average degree of the bacterial network, while reducing network complexity and inter-species connectivity. Soil metabolomics analysis revealed that vertical stratification altered the metabolic profiles of 27 metabolites, with the significantly changed metabolites primarily associated with carbohydrate and amino acid metabolism. In conclusion, the characteristics of the Qinghai Lake permafrost were regulated by regional vertical stratification, which further influenced microbial community structure and soil metabolic characteristics, thereby altering carbon and nitrogen stocks. Specifically, higher altitudes were more favorable for the retention of the carbon and nitrogen stocks of frozen soils in the Qinghai Lake basin.PMID:40005823 | DOI:10.3390/microorganisms13020459

Microorganisms. 2025 Feb 8;13(2):372. doi: 10.3390/microorganisms13020372.ABSTRACTTo investigate the regulatory effect of a bacteriocin-producing strain of Enterococcus faecalis DH9003 on the gut microbiota of mice, 15 healthy C57 male mice were randomly administered an equal volume of sterile normal saline (HD, control group, n = 7) and E. faecalis DH9003 (YD, treatment group, n = 8) via gavage. Metagenomic and metabolomic analyses were performed to determine the composition and metabolic function of the intestinal microbiota in mice. The results showed that the relative abundance of Firmicutes continuously increased over time in YD compared to HD. The number of E. faecalis DH9003 increased slowly and remained steady from days 7 to 28, indicating that E. faecalis DH9003 could colonize a considerable number of mouse guts via intragastric administration. Supplementation with E. faecalis DH9003 demonstrated a regulatory effect on the intestinal microbiota composition of mice, causing a shift in the relative abundance of Bacteroidetes and Firmicutes at the phylum level. In addition, a total of 2426 different metabolites were found in mouse feces, including 1286 and 1140 metabolites in positive and negative modes, respectively. Vitamin B6 and succinate were the most regulated and downregulated metabolites in negative ion mode, and the most upregulated and downregulated metabolites in positive ion mode were N-methyl-glutamic acid and N-octanoyl sphingosine. In conclusion, E. faecalis DH9003 can colonize mice gut, affecting the gut microbiota and metabolic competence. This strain therefore offers considerable potential for application as a probiotic.PMID:40005739 | DOI:10.3390/microorganisms13020372

Microorganisms. 2025 Feb 5;13(2):338. doi: 10.3390/microorganisms13020338.ABSTRACTPhotosynthetic microorganisms, such as microalgae, are remarkable for their ability to harness sunlight, fix carbon dioxide, and produce a variety of bioactive compounds. These organisms are pivotal in climate mitigation strategies as they can absorb carbon dioxide while generating valuable biomolecules. Among the diverse cultivation approaches, mixotrophic growth combines light energy with both inorganic and organic carbon sources, offering a unique strategy to enhance biomass production and metabolic diversity in microalgae. Here, microalgal species such as Nannochloropsis granulata, Phaeodactylum tricornutum, and Chlorella sp. were investigated for their potential applications under different cultivation methods, including phototrophy and mixotrophy. Mixotrophic conditions significantly improved biomass production across all tested species. Among these, Phaeodactylum tricornutum, a marine diatom, emerged as a promising candidate for bioactive compound production, exhibiting higher antiproliferative activity against human melanoma cells and antibacterial effects against Staphylococcus aureus. Importantly, Chlorella sp. was also found to possess antibacterial activity against Staphylococcus aureus, broadening its potential applications. Additionally, metabolomics analysis was performed on Chlorella sp. and Phaeodactylum tricornutum to identify the compounds responsible for the observed bioactivity. This study highlights the value of mixotrophic cultivation in enhancing the productivity and bioactivity of microalgae, positioning them as versatile organisms for sustainable biotechnological applications.PMID:40005705 | DOI:10.3390/microorganisms13020338

Microorganisms. 2025 Jan 26;13(2):279. doi: 10.3390/microorganisms13020279.ABSTRACTVarious bacterial strains with nitrate-reducing capacity (NRC), such as Haemophilus, Actinomyces, and Neisseria, are known to promote NH3 production, control pH in the oral cavity, and inhibit the growth of aciduric bacteria. However, experimental evidence on various estimated bacterial networks within the salivary microbiome is insufficient. This study aims to explore potential bacterial compositional competition observed within saliva samples from dental caries patients through a co-culture assay of mitis Streptococci, which is a primary colonizer in the salivary microbiome, and nitrate-reducing bacteria Haemophilus parainfluenzae. We investigated bacterial growth efficiency change by co-culture time using the qRT-PCR method. In addition, we applied LC/Q-TOF-based metabolites screening to confirm metabolic interactions between oral bacterial species and their association with dental caries from a metabolomics perspective. As a result, we first found that the nitrate reduction ability of H. parainfluenzae is maintained even in a co-culture environment with the mitis Streptococci group through a nitrate reduction test. However, nitrate reduction efficiency was hindered when compared with monoculture-based nitrate reduction test results. Next, we designed species-specific primers, and we confirmed by qRT-PCR that there is an obvious competitive relationship in growth efficiency between H. parainfluenzae and two mitis Streptococci (S. australis and S. sanguinis). Furthermore, although direct effects of nitrate reduction on competition have not been identified, we have potentially confirmed through LC/Q-TOF-based metabolite screening analysis that the interaction of various metabolic compounds synthesized from mitis Streptococci is driving inter-strain competition. In particular, we constructed a basic reference core-metabolites list to understand the metabolic network between each target bacterial species (H. parainfluenzae and mitis Streptococci) within the salivary microbiome, which still lacks accumulated research data. Ultimately, we suggest that our data have potential value to be referenced in further metagenomics and metabolomics-based studies related to oral health care.PMID:40005646 | DOI:10.3390/microorganisms13020279

Microorganisms. 2025 Jan 22;13(2):234. doi: 10.3390/microorganisms13020234.ABSTRACTBiofilms are one of the ways microorganisms exist in natural environments. In recent years, research has gradually shifted its focus to exploring the complexity and interactions of multi-species biofilms. A study showed that nine gut bacteria can form a multi-species biofilm on wheat fibers (M9 biofilm). However, the previous study did not clarify the reasons why M9 exhibited a better biofilm formation ability than the mono-species biofilms. In this study, the gene expression levels and metabolic accumulation of the M9 multi-species biofilm and biofilms of each individual bacterium were analyzed using transcriptomes and metabolomes. The differentially expressed genes (DEGs) showed that there were 740 common DEGs that existed in all of the nine groups, and they could regulate five pathways related to bacterial motility, cellular communication, and signal transduction. The metabolome results revealed that many peptides/amino acids and derivatives were produced in the M9 biofilm. Furthermore, purine metabolism was significantly enhanced in the M9 biofilm. L-arginine, l-serine, guanosine, and hypoxanthine were the common differentially accumulated metabolites (DAMs). The combined analysis of the transcriptomes and metabolomes showed that there were 26 common DEGs highly correlated with the four common DAMs, and they were involved in five metabolic pathways related to amino acids and purines. These results indicate that M9 can regulate multi-species biofilm formation by modulating genes related to bacterial motility, cellular communication, signal transduction, and the metabolism of amino acids and purines. This study provides insights into the interactions of microbial biofilms.PMID:40005603 | DOI:10.3390/microorganisms13020234

Pathogens. 2025 Jan 22;14(2):106. doi: 10.3390/pathogens14020106.ABSTRACTChagas disease, caused by Trypanosoma cruzi, is a parasitic zoonosis with significant health impacts, particularly in Latin America. While traditionally associated with vector-borne transmission, increased migration has expanded its reach into urban and non-endemic regions. Congenital transmission has become a critical route of infection, involving intricate maternal-fetal immune interactions that challenge diagnosis and treatment. This review synthesizes findings from three RNA-seq studies that explore the molecular underpinnings of congenital Chagas disease, emphasizing differentially expressed genes (DEGs) implicated in host-pathogen interactions. The DAVID tool analysis highlighted the overexpression of genes associated with the innate immune response, including pro-inflammatory cytokines that drive chemotaxis and neutrophil activation. Additionally, calcium-dependent pathways critical for parasite invasion were modulated. T. cruzi exploits the maternal-fetal immune axis to establish a tolerogenic environment conducive to congenital transmission. Alterations in placental angiogenesis, cellular regeneration, and metabolic processes further demonstrate the parasite's ability to manipulate host responses for its survival and persistence. These findings underscore the complex interplay between the host and pathogen that facilitates disease progression. Future research integrating transcriptomic, proteomic, and metabolomic approaches is essential to unravel the molecular mechanisms underlying congenital Chagas disease, with a particular focus on the contributions of genetic diversity and non-coding RNAs in immune evasion and disease pathogenesis.PMID:40005483 | DOI:10.3390/pathogens14020106

Medicina (Kaunas). 2025 Feb 4;61(2):262. doi: 10.3390/medicina61020262.ABSTRACTKidney transplantation stands as the preferred treatment for end-stage kidney disease, significantly improving both the quality and longevity of life compared to dialysis. In recent years, the survival rates for patients and grafts have markedly increased thanks to innovative strategies in desensitization protocols for incompatible transplants and advancements in immunosuppressive therapies. For kidney transplant recipients, preventing allograft rejection is of paramount importance, necessitating the use of immunosuppressive medications. Regular follow-up appointments are essential, as monitoring the function of the kidney allograft is critical. Currently, established biomarkers such as serum creatinine, estimated Glomerular Filtration Rate (eGFR), proteinuria, and albuminuria are commonly employed to assess allograft function. However, these biomarkers have limitations, as elevated levels often indicate significant allograft damage only after it has occurred, thereby constraining treatment options and the potential for restoring graft function. Additionally, kidney biopsies, while considered the gold standard for diagnosing rejection, are invasive and carry associated risks. Consequently, the identification and development of new, sensitive, and specific biomarkers like dd-cfDNA, microRNAs (e.g., miR-21, miR-155), and sCD30 for allograft rejection are crucial. To tackle this challenge, intensive ongoing research employing cutting-edge technologies, including "omics" approaches, like genomic techniques, proteomics, or metabolomics, is uncovering a variety of promising new biomarkers.PMID:40005378 | DOI:10.3390/medicina61020262