Search Results (53)

Background/Objectives: Genome-scale metabolic models (GSM) are key tools for predicting microbial physiology, yet species within the genus Lentilactobacillus remain largely unexplored. Lentilactobacillus kefiri DH5 is an obligately heterofermentative lactic acid bacterium with unique redox metabolism, but no curated GSM model exists for this species. This study aimed to generate the first GSM model for L. kefiri DH5, evaluate multiple reconstruction tools, and characterize metabolic features underlying its heterofermentative metabolism. Methods: Draft GSM models were generated from the L. kefiri DH5 genome annotation using five reconstruction tools. For each tool, gap-filling was performed on a CDM, followed by quality assessment using the MEMOTE. Manual curation was performed using the COBRApy library. Results: Among the five reconstructions, the KBase-derived draft demonstrated the highest quality and production potential for metabolites characteristic of heterofermentative fermentation. During manual curation of this model, reaction directions in central carbon metabolism and amino acid pathways were corrected. Analysis further identified an alternative NADH-regenerating glucose shunt via D-gluconate, supported by omics data and enzyme promiscuity considerations. Incorporation of this pathway resolved the redox imbalance and allowed the model to reproduce metabolic exchange profiles characteristic of obligate heterofermenters. Conclusions: We developed the first manually curated genome-scale model of L. kefiri DH5 and showed that the choice of reconstruction tool substantially affects model quality and predictive power. We also proposed an alternative glucose assimilation shunt via gluconolactone, which resolved the redox imbalance in the model and enabled representation of the heterofermentative metabolism. Full article

The clade Gluconacetobacter comprises eleven species originating from various sources such as rhizosphere soil, pink sugarcane mealybug, and vinegar. During sampling of organic vinegars, we isolated strain Hr-1-5, which exhibits high 16S rRNA gene sequence identities (≤98.6%) and low 16S-23S rRNA gene internal transcribed spacer (ITS) sequence identities (≤92.1%) with Gluconacetobacter species. Further genome analysis confirmed that strain Hr-1-5 is a distinct species, supported by an average nucleotide identity (ANIb) of ≤90.6% and an in silico DNA–DNA hybridization (dDDH) value of ≤46% compared with other recognized Gluconacetobacter species. Strain Hr-1-5 darkens the growth medium to a deep brown after 4–5 days of submerged cultivation and similarly colors agar medium after 5–6 days. In silico genome analysis suggests that the strain synthesizes pyomelanin. Phenotypically, it is distinguished from its closest Gluconacetobacter relatives by its ability to produce 5-keto-D-gluconic acid, but not 2-keto-D-gluconic acid, and by its capacity to grow on D-ribose, among other traits. These findings support the classification of strain Hr-1-5 as a novel species, for which we propose the name Gluconacetobacter brunescens sp. nov. Hr-1-5^T (=ZIM B1168^T = LMG 33629^T). Strain Hr-1-5 is of biotechnological interest for its pigment production and enables the in situ production of colored cellulose in a co-culture with a cellulose-producing acetic acid bacterium. Full article

The decline in eggshell quality of aged laying hens represents a major economic challenge in poultry production. While a 28 h ahemeral light cycle has been shown to improve eggshell quality, its underlying mechanism remains unclear. This study randomly assigned 260 74-week-old Hy-Line Brown laying hens to two light cycle groups, a normal 24 h cycle group (16L:8D) and a 28 h ahemeral cycle group (16L:12D). Each treatment comprised 130 hens divided into two replicate groups. The trial lasted 16 weeks. We systematically analyzed circadian rhythms of gut microbiota and serum metabolites using 16S rRNA sequencing and untargeted metabolomics. Compared with the 24 h cycle, the 28 h cycle significantly enhanced eggshell thickness by 0.04 mm and 0.02 mm, and eggshell strength by 4.19 N and 4.76 N at 79 and 84 wk, respectively. Mechanistically, the 28 h light cycle remodeled the circadian rhythms of gut microbiota, increasing their richness and diversity, and altered the rhythmic patterns of serum metabolites. We identified nine microbial genera and three hundred seventy metabolites that exhibited opposite rhythmic patterns under the two light cycles. These changes were primarily enriched in pathways related to amino acid, carbohydrate, lipid, and energy metabolism. Correlation analysis further revealed strong associations between key microbes and functional metabolites. Weissella promotes calcium deposition in eggshells through synergistic interactions with calcium chelators such as gluconic acid and threonine acid. Meanwhile, YRC22 and Paludibacter synergistically support membrane formation substances, thereby promoting the proliferation of uterine epithelial cells and eggshell formation. Our findings indicate that the 28 h ahemeral light cycle improved eggshell quality in aged hens by remodeling the circadian rhythms of gut microbiota and metabolites, thereby synergistically enhancing calcium ion absorption and uterine tissue health. This provides a novel theoretical basis and practical direction for improving late-phase egg quality through light management strategies. Full article

Using renewable D-gluconic acid δ-lactone as the starting material, two novel glucosamide-based organosilicon quaternary ammonium surfactants (2/3SiDDGPBH) were synthesized through an environmentally friendly three-step process involving amidation, hydrophobic modification, and quaternization. Comprehensive characterization demonstrated their exceptional performance: surface tension reduction to 33.4 mN/m (2SiDDGPBH) and 33.64 mN/m (3SiDDGPBH), uniform spherical micelles (1–10 nm and 30–100 nm) were formed, and outstanding foam properties with 3SiDDGPBH developed, showing superior foamability and stability. Material modification tests on polymethyl methacrylate (PMMA) plates, mature acacia leaves, oilpaper, vegetable-tanned top-grain leather, and melamine-formaldehyde resin (MFR) faced with plywood revealed excellent spreading performance and durability, particularly for 3SiDDGPBH-treated MFR plywood, which maintained excellent spreading performance even after 80 washing cycles. Scanning electron microscopy (SEM) analysis confirmed that the Si wt% of MFR plywood treated with 2/3SiDDGPBH and scrubbed MFR plywood both exhibited a significant increase, and the 3SiDDGPBH-treated MFR plywood demonstrated superior bonding properties. These surfactants combine low surface tension, excellent foaming properties, and outstanding spreading performance, demonstrating broad application prospects in fields such as pesticide adjuvants, industrial and household cleaning agents, cosmetics, oilfield extraction, textile printing and dyeing, and functional coatings. Full article

Penicillium expansum is an acidogenic fungal species that belongs to the phylum Ascomycota. During the infection and colonization of host fruits, P. expansum can efficiently express glucose oxidase (GOX) and oxidize β-D-glucose to generate gluconic acid (GLA). In this study, the bioinformatics analysis method was employed to predict and analyze the function of the GOX protein. In addition, a comprehensive assessment was conducted on the P. expansum GOX coding gene GOX2, and the expression response rules of GOX2 under different external stress environments were explored. The results show that GOX is an unstable hydrophilic protein. It is either an integrated membrane protein (such as a receptor or channel) that is directly anchored to the membrane through a transmembrane structure or a non-classical secreted protein that is secreted extracellularly. RNA-seq data analysis shows that the GOX2 gene is regulated by multiple environmental factors, including pH, temperature, carbon base, and chemical fungicides. The expression level of GOX2 reaches its maximum value under alkaline conditions (pH 8–10) and at approximately 10 °C. Using starch as the carbon source and adding sodium propionate or potassium sorbate has the effect of inhibiting the expression of the GOX2 gene. The analysis of the function of the GOX protein and the characteristics of the GOX2 gene in P. expansum provides new insights into the glucose oxidase-encoding gene GOX2. The research results provide significant value for the subsequent development of new disease resistance strategies by targeting the GOX2 gene and reducing post-harvest disease losses in fruits. Full article

In northern China’s arid and semi-arid regions, evergreen trees demonstrate significant cold tolerance to natural low-temperature stress during winter. However, the metabolic strategies and their associated properties underlying their overwintering adaptation remain incompletely elucidated. This study aims to reveal the metabolic properties of natural low-temperature adaptation strategies in five evergreen trees through metabolomic analysis and to identify key metabolites and their dynamic variation patterns. The GC-TOF-MS platform was used to investigate seasonal differential metabolites in five evergreen trees across January, April, July, and October and further explore core differentially expressed metabolites responsive to low-temperature stress. The results demonstrated that the seasonal changes in the chlorophyll content of five evergreens exhibited distinct patterns, that significant differences were observed between Juniperus sabina L. and Picea meyeri R., Ammopiptanthus mongolicus M., Buxus sinica var. parvifolia M.Cheng, and Pinus tabuliformis C., and that no significant differences were found among the other tree species. A total of 427 metabolites were detected in the metabolome; when assessing seasonal dynamics, it was found that the types of differentially expressed metabolites in the five evergreens underwent significant changes. In spring, the differentially expressed metabolites included some carbohydrates, alcohols, organic acids, and lipids. During summer and autumn, the largest number of differentially expressed metabolites accumulated, mainly including carbohydrates, organic acids, and amino acid compounds. In winter, while Picea meyeri primarily accumulated carbohydrates, the remaining four species mainly accumulated organic acids, along with a small number of alcohols, phenylpropanoids, and polyketides. Three shared carbohydrate metabolites, L-threose, galactinol, and gluconic lactone, were commonly downregulated across all species. Additionally, coniferous trees collectively accumulated 3,6-anhydro-D-galactose, showing downregulation. The KEGG enrichment analysis of winter-accumulated metabolites revealed significant associations with the pentose phosphate pathway, amino acid metabolism, phenylpropanoid biosynthesis, the tricarboxylic acid cycle, and ascorbate–aldarate metabolism pathways. Through comparative analysis with the summer growth season, we ultimately identified the core differentially expressed metabolites of the five evergreens, providing potential metabolic markers for the breeding of cold-tolerant species. In summary, these findings provide critical metabolomic insights into how plants adapt to low temperatures, significantly enhancing our understanding of the metabolic foundations of cold tolerance in evergreen species. Full article

The genera Komagataeibacter and Novacetimonas comprise industrially important species that produce various foods, nanocellulose, acetan-like polysaccharides, enantioselective sugars, and other valuable products. Here, we describe two novel strains, Hr1 and Jurk4, isolated from pear and apple-grape organic vinegars that showed very high (≥99.39%) 16S rRNA gene sequence identities to species of the Komagataeibacter and Novacetimonas genera, respectively. However, analysis of the 16S-23S rRNA gene internal transcribed spacer (ITS) sequences revealed only 92.6% sequence identity between the Hr1 strain and its closest relative, Komagataeibacter sucrofermentans LMG 18788^T, and 93.8% sequence identity between the Jurk4 strain and its closest relative, Novacetimonas cocois JCM 31140^T. Further whole-genome analysis showed for both strains an average nucleotide identity (ANI) below 94% and an in silico DNA–DNA hybridization (dDDH) value of less than 70% to their closest species, supporting their distinction as novel species. The strain Hr1 can be phenotypically differentiated from its closest Komagataeibacter species based on its ability to utilize (NH₄)₂SO₄ as the sole nitrogen source in Asai medium with D-glucose and its inability to grow with 1-propanol as a sole carbon source. The strain Jurk4 can be differentiated from other Novacetimonas type strains based on its ability to produce 5-keto-D-gluconic acid, its growth in a medium with glycerol as the sole carbon source, and its inability to grow in an Asai medium with D-glucose. Both strains produce cellulose and possess clusters for acetane-like polysaccharide production, although of different types, which makes them industrially relevant. Based on these findings, we propose Komagataeibacter piraceti sp. nov. Hr1^T (=ZIM B1167^T = LMG 33628^T) and Novacetimonas labruscae sp. nov. Jurk4^T (=ZIM B1166^T = LMG 33630^T) as two novel members of the acetic acid bacteria group. Full article

A class of hybrid molecularly imprinted polymeric nanoparticles (nanoMIPs) comprising the in situ formation of gold nanoparticles (AuNPs) immobilised in a molecularly imprinted D-gluconate polymer has been designed with the objective of attempting the electrochemical quantification of gluconic acid (GA) in a wine setting. The imprinted polymers were synthesised in the presence of AuNP precursors in a pre-polymerisation mixture, which were confined to one another during the polymerisation of the chains. This allowed the formation of hybrid electroactive responsive imprinted nanoparticles (hybrid AuNPs@GA-nanoMIP), which exhibited enhanced electron conductivity. The morphological characterisation of the produced nanoMIPs revealed a fully decorated Au spherical surface of 200 nm in diameter. This resulted in a large active surface area distribution, as well a pronounced electrochemical peak response at the commercial screen-printed platinum electrode (SPPtE), accompanied by enhanced electron kinetics. The AuNPs@GA-nanoMIP sensor demonstrated the ability to detect a broad range of GA concentrations (0.025–5 mg/mL) with exceptional selectivity and reproducibility. The calibration curves were fitted with different isotherm models, such as the Langmuir, Freundlich and Langmuir–Freundlich functions. Moreover, the efficacy of the detection method was demonstrated by the recovery rates observed in real samples of Italian red wine. This research contributes to the development of a robust and reliable electrochemical sensor for the on-site determination of gluconic acid in food analysis. Full article

The basidiomycete Crucibulum laeve strain LE-BIN1700 (Agaricales, Nidulariaceae) is able to grow on agar media supplemented with individual components of lignocellulose such as lignin, cellulose, xylan, xyloglucan, arabinoxylan, starch and pectin, and also to effectively destroy and digest birch, alder and pine sawdust. C. laeve produces a unique repertoire of proteins for the saccharification of the plant biomass, including predominantly oxidative enzymes such as laccases (family AA1_1 CAZymes), GMC oxidoreductases (family AA3_2 CAZymes), FAD-oligosaccharide oxidase (family AA7 CAZymes) and lytic polysaccharide monooxygenases (family LPMO X325), as well as accompanying acetyl esterases and loosenine-like expansins. Metabolomic analysis revealed that, specifically, monosaccharides and carboxylic acids were the key low molecular metabolites in the C. laeve culture liquids in the experimental conditions. The proportion of monosaccharides and polyols in the total pool of identified compounds increased on the sawdust-containing media. Multiple copies of the family AA1_1, AA3_2, AA7 and LPMOs CAZyme genes, as well as eight genes encoding proteins of the YvrE superfamily (COG3386), which includes sugar lactone lactonases, were predicted in the C. laeve genome. According to metabolic pathway analysis, the litter saprotroph C. laeve can catabolize D-gluconic and D-galacturonic acids, and possibly other aldonic acids, which seems to confer certain ecological advantages. Full article

Coccidiosis, caused by different species of Eimeria parasites, is an economically important disease in poultry and livestock worldwide. This study aimed to investigate the changes in the ileal microbiota and fecal metabolites in chickens after repeated infections with low-dose E. mitis. The chickens developed solid immunity against a high dose of E. mitis infection after repeated infections with low-dose E. mitis. The composition of the ileal microbiota and the metabonomics of the Eimeria-immunized group and the control group were detected using 16S rRNA sequencing and liquid chromatography–mass spectrometry (LC-MS). The relative abundance of Neisseria, Erysipelotrichaceae, Incertae sedis, Coprobacter, Capnocytophaga, Bifidobacterium, and the Ruminococcus torques group declined in the Eimeria-immunized chickens, whereas Alloprevotella, Staphylococcus, Haemophilus, and Streptococcus increased. Furthermore, 286 differential metabolites (including N-undecylbenzenesulfonic acid, 1,25-dihydroxyvitamin D3, gluconic acid, isoleucylproline, proline, and 1-kestose) and 19 significantly altered metabolic pathways (including galactose metabolism, ABC transporters, starch and sucrose metabolism, the ErbB signaling pathway, and the MAPK signaling pathway) were identified between the Eimeria-immunized group and the control group. These discoveries will help us learn more about the composition and dynamics of the gut microbiota as well as the metabolic changes in chickens infected with Eimeria spp. Full article

This review analyzes the use of magnetite-based catalysts in various oxidation reactions. It is shown that magnetite-based catalysts are the most promising candidates from the standpoint of easy separation from the reaction zone and reusability. Diverse examples of the use of magnetite-based composites are discussed, including the following reactions: partial oxidation of methane to formaldehyde; the oxidation of cycloalkanes into alcohols and ketones; the oxidation of alkenes and alcohols with the major focus made on benzylic alcohol oxidation; oxidative cracking of alkenes; Fenton-type reactions with H₂O₂ as a benign oxidant; the removal of dyestuff in water (including wastewater by oxidation); reactions of sulfides and thiols; the oxidation of 5-hydroxymethylfurfural as a platform chemical to 2,5-diformylfuran; the oxidation of D-glucose to D-gluconic acid; and the electrocatalytic oxidation of methanol and ethanol. The most important and best-studied applications of magnetic nanoparticles in the oxidation reactions are believed to be the oxidation of diverse benzylic alcohols and D-glucose, and Fenton-like reactions aiming at the removal of S- and N-compounds from ware and fuels. Magnetic nanocomposites are determined as the materials meeting a range of criteria: (1) they should be magnetic, (2) they contain nanoparticles, and (3) they consist of two (or more) nanocomponents. The core–shell materials with magnetic nanoparticles used as a core or as decorating nanoparticles are discussed in the review. Three main types of magnetic nanocomposites can be distinguished: (1) the systems where the magnetic phase is active in the considered reaction, for instance, Fenton-like oxidation; (2) the systems containing active metal nanoparticles supported onto the magnetic nanoparticles; and (3) materials with magnetic nanoparticles as a core coated with one or two shells (porous or non-porous), with the magnetic nanoparticles being active or not in the title reaction. Magnetic nanoparticles exhibit a number of advantages compared with supported non-magnetic catalysts of oxidation reactions. The advantages include the possibility of separation from the reaction medium (5–10 times) without a significant loss of the activity, their non-toxicity, low cost, and availability, and the easy preparation of these materials. The drawbacks may include the leaching of active components; a decrease in saturation magnetization in comparison with the bulk magnetite; a limited accessibility of active sites due to diffusion through the shells; the complicated composition and structure of the nanomaterials; a decrease in the activity and specific surface area; and a limited number of magnetic compounds with acceptable characteristics. Nevertheless, the advantages of magnetic nanocatalysts stimulate their wide use in liquid-phase oxidation reactions, which will be discussed in the review. Future perspectives on the use of magnetic composites are considered. Full article

Camellia luteoflora is a rare and endangered plant endemic to China. It has high ornamental and potential economic and medicinal value, and is an important germplasm resource of Camellia. To understand the distributions and differences in metabolites from different parts of C. luteoflora, in this study, we used liquid chromatography–tandem mass spectrometry (LC–MS/MS) to examine the types and contents of chemical constituents in five organs of C. luteoflora: roots, stems, leaves, flowers, and fruits. The results showed that a total of 815 metabolites were identified in the five organs and were classified into 18 main categories, including terpenoids (17.1%), amino acids (10.4%), flavonoids (10.3%), sugars and alcohols (9.8%), organic acids (9.0%), lipids (7.1%), polyphenols (4.8%), alkaloids (4.8%), etc. A total of 684 differentially expressed metabolites (DEMs) in five organs were obtained and annotated into 217 KEGG metabolic pathways, among which metabolic pathways, ABC transporters, the biosynthesis of cofactors, and the biosynthesis of amino acids were significantly enriched. In DEMs, flowers are rich in flavonoids, polyphenols, organic acids, and steroids; fruits are rich in amino acids, alkaloids, vitamins, and xanthones; stems are rich in lignans; and leaves have the highest relative content of phenylpropanoids, ketoaldehydic acids, quinones, sugars and alcohols, terpenoids, coumarins, lipids, and others; meanwhile, the metabolite content is lower in roots. Among the dominant DEMs, 58 were in roots, including arachidonic acid, lucidone, isoliquiritigenin, etc.; 75 were in flowers, including mannose, shikimic acid, d-gluconic acid, kaempferol, etc.; 45 were in the fruit, including pterostilbene, l-ascorbic acid, riboflavin, etc.; 27 were in the stems, including salicylic acid, d-(-)-quinic acid, mannitol, (-)-catechin gallate, etc.; there was a maximum number of 119 dominant metabolites in the leaves, including oleanolic acid, l-glucose, d-arabitol, eugenol, etc. In sum, the rich chemical composition of C. luteoflora and the significant differences in the relative contents of metabolites in different organs will provide theoretical references for the study of tea, flower tea, edible oil, nutraceuticals, and the medicinal components of C. luteoflora. Full article

Cyclocarya paliurus tea, also known as “sweet tea”, an herbal tea with Cyclocarya paliurus leaves as raw material, is famous for its unique nutritional benefits and flavor. However, due to the unique “bittersweet” of Cyclocarya paliurus tea, it is still unable to fully satisfy consumers’ high-quality taste experience and satisfaction. Therefore, this study aimed to explore metabolites in Cyclocarya paliurus leaves during their growth period, particularly composition and variation of sweet and bitter taste compounds, by combining multi-platform metabolomics analysis with an electronic tongue system and molecular docking simulation technology. The results indicated that there were significant differences in the contents of total phenols, flavonoids, polysaccharides, and saponins in C. paliurus leaves in different growing months. A total of 575 secondary metabolites were identified as potential active metabolites related to sweet/bitter taste using nontargeted metabolomics based on UHPLC-MS/MS analysis. Moreover, molecular docking technology was utilized to study interactions between the candidate metabolites and the sweet receptors T1R2/T1R3 and the bitter receptors T2R4/T2R14. Six key compounds with high sweetness and low bitterness were successfully identified by using computational simulation analysis, including cis-anethole, gluconic acid, beta-D-Sedoheptulose, asparagine, proline, and citrulline, which may serve as candidates for taste modification in Cyclocarya paliurus leaves. These findings provide a new perspective for understanding the sweet and bitter taste characteristics that contribute to the distinctive sensory quality of Cyclocarya paliurus leaves. Full article

Gold nanoparticle (AuNP) fabrication via the oxidation of D-glucose is applied for detecting two foodborne pathogens, Enterococcus faecium (E. faecium) and Staphylococcus aureus (S. aureus). D-glucose is used as a reducing agent due to its oxidation to gluconic acid by sodium hydroxide (NaOH), resulting in the formation of AuNPs. Based on this mechanism, we develop AuNP-based colorimetric detection in conjunction with loop-mediated isothermal amplification (LAMP) for accurately identifying the infectious bacteria. Here, Au⁺ ions bind to the base of double-stranded DNA. In the presence of D-glucose and NaOH, the LAMP amplicon-Au⁺ complex maintains its bound state at 65 °C for 10 min while it is reduced to AuNPs in a dispersed form, exhibiting a red color. We aimed to pre-mix D-glucose with LAMP reagents before amplification and induce successful colorimetry without inhibiting amplification to simplify the experimental process and decrease the reaction time. Therefore, the entire process, including LAMP and colorimetric detection, is accomplished in approximately 1 h. The limit of detection of E. faecium and S. aureus is confirmed using the introduced method as 10¹ CFU/mL and 100 fg/μL, respectively. We expect that colorimetric detection using D-glucose-mediated AuNP synthesis offers an application for simple and immediate molecular diagnosis. Full article

Two isolates of Roseateles were discovered in soil samples collected from Uiwang-si, Gyeonggi-do, Republic of Korea. These isolates exhibited rod-shaped morphology and were facultatively anaerobic, non-motile, and tested positive for oxidase and catalase. Designated as strains R3-3^T and R3-11, their growth was hindered by NaCl concentrations exceeding 0.5%, while their optimal growth conditions were observed at temperatures ranging from 25 °C to 30 °C and pH levels between 7.0 and 9.0. Both strains exhibited positive results for the hydrolysis of Tween 80 and DNA, but tested negative for starch, casein, chitin, and gelatin hydrolysis. Additionally, they assimilated L-Arabinose, D-mannitol, and D-Maltose, while exhibiting negative results for the fermentation of D-glucose, esculin ferric citrate, D-mannose, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. The DNA G+C content of strain R3-3^T was measured at 67.5 mol%. Comparative analysis revealed that the average nucleotide identity (ANI) values between R3-3^T and the Roseateles type strains ranged from 75.14% to 78.30% while the digital DNA-DNA hybridization (dDDH) values ranged from 20.70% to 22.70%. Consequently, based on comprehensive genomic, chemotaxonomic, phenotypic, and phylogenomic evaluations, the isolated strains have been designated as a new species within the genus Roseateles, named Roseateles agri sp. nov. (with type strain R3-3^T = KACC 23678^T = NBRC 116681^T). Full article