Transcriptomics analysis provides insights into the molecular response of the clam Cyclina sinensis to Vibrio infection under heat stress.

Investigation of flavor formation mechanism of broad bean paste fermented by Bacillus amyloliquefaciens SCPC-RY2021.

Biosynthetic reuterin improved the intestinal health in pigs.

Understanding the probiotic potential of a healthy human vaginal flora, Lactobacillus gasseri K9: genomic and in vitro aspects

Amoxicillin and copper affect humification during compost: Insight into dissolved organic matter and bacterial community succession.

Uptake, metabolism, and underlying mechanisms of neonicotinoid insecticides in rice plants (Oryza sativa L.).

The poultry industry faces increasing demand for sustainable production aligned with meat quality and animal welfare. This study examined effects of space allowance (39 vs. 21kg/m2) and dietary fibre (DF) supplementation (control vs. DF) on broiler pectoralis major muscle using mass spectrometry-based proteomics under higher-welfare conditions. While yield characteristics were unaffected, reduced space allowance significantly increased intramuscular fat and altered the proteome, with enrichment of proteins in oxidative phosphorylation, transcriptional stress and shifts in carbohydrate metabolism. Broilers receiving DF exhibited lower physical activity and feeding behaviours, with proteomic profiles linked to glycolysis, glycogen turnover and muscle architecture, as well as with reduced drip loss regardless of space allowance. Under higher space, DF induced broader proteomic adaptations, including cytoskeletal remodelling, lipid biosynthesis regulation and vascular homeostasis. These findings highlight how husbandry factors interact to shape meat phenotypes, offering a molecular framework to support quality-focused, welfare-aligned and environmentally conscious meat production.

The effects of berberine (BBR) on intestinal health suffering from soybean meal (SBM)-induced enteritis (SBMIE) in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) were investigated in this study, focusing specifically on oxidant-antioxidant capacity, intestinal morphology, microbiota homeostasis and tryptophan catabolites. A total of 270 individuals with the initial body weight (IBW) of 23.27 ± 0.60 g were randomly divided into 9 tanks at the density of 30 fish per tank. Three diets, the SBM diet (75% of fish meal substituted by SBM, SBM), BBR1 (75 mg/kg BBR was added to the SBM diet, BBR1) and BBR2 diet (150 mg/kg BBR was added to the SBM diet, BBR2), were used to feed fish for 42 d. The results indicated that the final body weight (FBW), weight gain rate (WGR) and specific growth rate (SGR) were all significantly increased in BBR2 group compared with SBM group (P < 0.05). Intestinal barrier proteins and genes (ZO-1 and occludin) expression (P < 0.05) and intestinal interleukin-10 (IL-10) content (P = 0.001) were all greatly improved with BBR administration, especially in the BBR2 group. The apoptosis related genes (caspase 3 and caspase 9) (P < 0.05) of intestinal epithelium cells were also significantly reduced by dietary BBR compared with SBM group. Comparative analysis of intestinal microbial composition and tryptophan catabolites between the SBM group and BBR2 group revealed that BBR significantly ameliorated the imbalance of intestinal microbiota and improved the intestinal tryptophan catabolites, especially reflected in the relative abundance of Romboutsia and the levels of L-5-hydroxytryptophan (L-5-HTP), indole-3-acetic acid (IAA) and kynurenine (KYN) in intestinal contents (P < 0.05). As a result, the aryl hydrocarbon receptor (AhR) signaling was then activated. Correlation analyses showed that the relative abundance of Romboutsia was positively correlated with IAA and KYN levels in the intestinal contents (P < 0.05), and negatively correlated with interleukin-1 beta (IL-1β) and interleukin-6 (IL-6) levels in hindgut (P < 0.01). The levels of L-5-HTP, IAA, and KYN in intestinal contents were positively correlated with key factors of hindgut AhR signaling pathway, tight junctions (TJs) and anti-inflammatory cytokines (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) functional prediction results showed that the intestinal microbial functions were mainly enriched in metabolic pathways, including amino acid metabolism, carbohydrate metabolism, and metabolism of cofactors and vitamins. In conclusion, BBR ameliorated SBMIE in hybrid yellow catfish by reducing oxidative stress, enhancing antioxidant and anti-inflammatory capacity, alleviating intestinal pathological damage and microbial dysbiosis. The microbiota-tryptophan catabolite-AhR axis may play an essential role in this protective process.

Comparative genomics of Idotea balthica populations: Evolutionary divergence between Mediterranean and Baltic lineages.

Superior ethylene biosynthesis in hexaploid Salix rehderiana induces higher ERF105 expression, enabling greater lead (Pb) tolerance compared to diploids.

Prebiotic potential of turmeric and fingerroot polysaccharides: modulation of human gut microbiota and metabolite profiles in in vitro colonic fermentation

Nano-selenium improves the humification process of cattle dung during composting by regulating carbohydrate-active enzymes and carbohydrate metabolism

Streptococcus mutans is a key cariogenic pathogen of dental caries due to its strong ability to synthesize extracellular glucans and form biofilms. Glucosyltransferases, encoded by gtfB/C/D genes in S. mutans, are responsible for producing biofilm exopolysaccharides (EPS) and are considered to be critical virulence factors. Previous studies have highlighted the roles of various regulatory factors of gtf genes in S. mutans. Here, we investigated the role of the global transcriptional regulator CcpA encoded by ccpA in regulating the EPS synthesis and biofilm formation of S. mutans. A ccpA in-frame deletion strain was observed to develop shiny, round colonies and longer cell length. In addition, the deletion of ccpA resulted in impaired growth, diminished synthesis of EPS, and reduced biofilm formation. Transcriptome analysis revealed that differentially expressed genes in the ccpA deletion strain were significantly enriched in pathways of carbohydrate transport and metabolism, in which the expressions of gtfB and gtfC were downregulated markedly. Electrophoretic mobility shift assays confirmed that CcpA directly binds to the promoter sequences of gtfB and gtfC, with a higher affinity for gtfC. Moreover, the expression level of ccpA in part explained differences in the ability to synthesize sufficient EPS and form stable biofilm in clinically isolated strains. These findings highlight that CcpA plays a crucial role in the EPS production and biofilm formation of S. mutans through directly binding to the promoter regions of gtfB and gtfC. This study provides novel insights into the pathogenic mechanisms of S. mutans and potential strategies for the prevention and treatment of dental caries.

Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.

Deceased-donor kidneys experience cellular stress before undergoing transplantation. To alleviate this, preservation techniques were developed, including normothermic machine perfusion (NMP). Here, we performed kidney NMP on discarded human kidneys for up to 24 h. Volume management was regulated either by urine recirculation (UR) or urine replacement (NUR) with Ringer's lactate. Notably, UR led to longer perfusion times compared with NUR. To investigate kidney NMP metabolic traits with or without UR over time, we performed longitudinal metabolomics analyses of perfusates of 8 NMP kidneys by 2-dimensional gas chromatography mass spectrometry (GCxGC-MS). Over 600 metabolic features were profiled, from which 74 were identified and 54 consistently quantified across 26 perfusate samples. Most notably, elevated levels of disaccharides (different isomers), hydroxy-purines, urea, glutamate, and amino acids are associated with the perfusion factor UR. Moreover, donor estimated glomerular filtration rate correlated significantly with the accumulation of lactate and gluconate. Most strikingly, lactate levels seemed to be more balanced in UR-NMP perfusate, which otherwise accumulated rapidly within the first 6 h. Kidney preservation by NMP was previously limited to hours. UR-NMP affected kidney energy homeostasis, carbohydrate and purine metabolism, and the urea and citric acid cycles. These insights add value to explain how urine-driven adaptations contribute to prolonged kidney function under NMP.

An emerging body of evidence has highlighted the complex interplay among obesity, insulin resistance, and the gut microbiota. This observational study aimed to evaluate differences in intestinal microbiome profiles between individuals with obesity, with and without insulin resistance. Twenty individuals with obesity aged 20-50 years were enrolled and categorized according to insulin resistance status (N = 10 per group), as determined using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). Fasting blood samples were collected and analyzed for glucose, lipid profiles, insulin, free fatty acids, and high-sensitivity C-reactive protein (hsCRP). Fecal DNA was extracted, and its quantity and quality were assessed.The V3-V4 region of 16s rRNA was amplified using specific primers, purified, and sequenced on the MiSeq Illumina platform with paired-end reads. The two groups showed notable disparities in fasting glucose (p=0.002), insulin (p<0.001), and HOMA-IR indices (p<0.001). While Alpha diversity remained comparable between groups when assessed using Shannon’s and Simpson’s indexes (but was significant for the Chao1 index), beta diversity was lower in the insulin-resistant group (p<0.05). Short-chain fatty acid-producing bacteria such as members of Lachnospiraceae family, Oscillospirales , and Faecalibacterium prausnitzii , were significantly enriched in insulin-sensitive individuals. In contrast, Alistipes putredenis was more abundant in those with insulin resistance. KEGG Orthology (KO) analysis revealed distinct functional enrichment: the Insulin Resistance group was enriched in carbohydrate metabolism pathways (e.g., glycolysis/gluconeogenesis, TCA cycle), while the Insulin Sensitive group showed more diverse metabolic activity, including amino acid and fatty acid metabolism, butyrate metabolism, and select carbohydrate pathways. These findings contribute to understanding the role of gut microbiota in metabolic heterogeneity associated with insulin resistance in obesity. • Beta diversity was significantly different between the groups, being lower in the Insulin- Resistance (IR) group, which indicates a distinct microbial community structure. • The study found two dominant enterotypes: the Prevotella genus and the Bacteroides genus. • The Insulin-Sensitive (IS) group was enriched in beneficial, short-chain fatty acid-producing bacteria, specifically members of the Lachnospiraceae family and species such as Faecalibacterium prausnitzii. • The Insulin-Resistant (IR) group had a higher abundance of proinflammatory bacteria, including Alistipes putredinis (also called Alistipes obesi ) and Escherichia–Shigella. • Predicted Functions: The microbiota in the IR group was enriched in carbohydrate metabolism pathways, whereas the IS group's microbiota showed greater activity in amino acid, fatty acid, and butyrate metabolism.

Draft genome sequence of Leuconostoc mesenteroides isolated from fermented kodo millet: Genomic insights into probiotic and anti-diabetic potential.

Bridged bicyclic systems, characterized by their distinctive three-dimensional topology and inherent ring strain, confer unique spatial configurations and chemical reactivity. Increasing the molecular three-dimensionality and the fraction of sp3-hybridized carbon atoms (Csp3) in lead compounds enhances drug-like behavior. In particular, the norbornene scaffold-an archetypal bridged bicyclic framework-offers significant potential for pesticide optimization by enhancing bioactivity. We designed and synthesized 54 novel stereoisomeric derivatives containing norbornene and evaluated their antifungal activity. The bioassay results showed that most of the target compounds possessed great in vitro antifungal activity against a wide range of plant pathogenic fungi. For example, half-maximal effective concentration (EC50) = 0.31 mg/L of compound Y15 against Botrytis cinerea was comparable with that of the commercially available drug dimethachlon (EC50 = 0.37 mg/L), and 150.8-fold higher than norbornene (EC50 = 46.74 mg/L). In addition Y15 showed great aquatic biosafety, with an acute toxicity half-maximal lethal concentration (LC50) > 80.0 mg/L to zebrafish 48 h (superior to dimethachlon (LC50 = 11.90 mg/L)). RNA sequencing and quantitative reverse transcription polymerase chain reaction experiments showed that compound Y15 affected a large number of differentially expressed genes related to carbohydrate metabolism, oxidoreductase activity and membrane composition, and had a relatively large number of genes involved in microbial metabolic activity and the biosynthesis of secondary metabolites. We reported a series of novel dicarboximide fungicides containing a bridging ring structure that provided a new basis for the molecular design and mechanistic study of stereoisomeric fungicides. © 2026 Society of Chemical Industry.

The coexistence of non-starch polysaccharides and resistant starch (RS) impacts the physiological functions of dietary fiber, especially the availability of dietary fiber with some specific structures (e.g. insoluble dietary fiber, IDF). Therefore, three complexes with different ratios of RS/IDF from tiger nuts were prepared, followed by an investigation of their corresponding physicochemical and structural properties, as well as the regulatory role in gut microbiota. The results indicated that the complex with RS/IDF ratio of 5/95 (H-IDF) had the greatest water retention, water swelling and oil retention capacities. All three complexes had a similar amylopectin/amylose ratio, which attenuated the impact on microbial fermentation. However, the complex with RS/IDF ratio of 40/60 (L-IDF) had the greatest potential to promote microbial fermentation demonstrated by severe morphological damage. Furthermore, the fermentation of L-IDF led to the greatest generation of acetate and butyrate, but the lowest generation of isobutyrate. Meanwhile, the fermentation of L-IDF enhanced Prevotella abundance, accompanied by a reduced Firmicutes/Bacteroidetes ratio and pathogenic bacteria in terms of Proteobacteria and Escherichia-Shigella. The increased butyrate levels during 24 h fermentation might be primarily due to the enhanced abundance of Faecalibacterium in the early phases and Bifidobacterium in the later phases. The further analysis of functional prediction consistently supported a significantly up-regulated carbohydrate metabolism and down-regulated amino acid metabolism following L-IDF fermentation. This study might highlight a new approach for designing complex carbohydrates with targeted intestinal health functions via the regulation of the RS/IDF ratio. © 2026 Society of Chemical Industry.

The health threat of wild animals by Rank I ARGs from habitat soils: Metagenomic and metabolomic evidence.