Mint is considered to have a greater number of phenolic acids, flavonoids, antioxidants and other bioactive components, and is widely used as food, medicine, spices, and flavoring agents. Thus, chemical composition is an important parameter for assessing the quality of mint. In this study, two mint cultivars were sampled, purple mint and green mint. The purple mint had much higher anthocyanin and total flavone content compared with green mint. Transcriptome and metabolome technique were employed to elucidate the regulation network of mint pigment and flavone. A total of 167,901 unigenes were obtained by high-throughput RNA-Seq and 34,608 genes were differentially expressed. The differentially expressed genes (DEGs) were mainly involved in lignin metabolic process and flavonoid biosynthetic process. A total of 143 differentially expressed metabolites (DEMs) were enriched in isoflavonoid biosynthesis, flavonoid biosynthesis, flavone and flavonol biosynthesis, and anthocyanin biosynthesis pathways. The co-analysis results of DEGs and DEMs showed that the flavone and flavonol biosynthesis pathway (ko00944) contained the most DEMs, followed by flavonoid biosynthesis pathway (ko00941) and anthocyanin biosynthesis pathway (ko00942). Furthermore, the most important nine genes and metabolites were screened using O2PLS model. The results will provide a theoretical basis for revealing pigment and flavone biosynthesis network of mint.

Different soil nutrients affect plant metabolites accumulation characteristics. The main soil nutrients and their correlation with Pepino metabolites were investigated in this study to evaluate differences between greenhouses on the Loess Plateau in northwest China. A total of 269 Pepino metabolites in the fruits were identified using a UPLC-QTOF-MS approach from plants grown in three major Pepino growing regions. Their differential distribution characteristics were analyzed. 99 metabolites differed among the Pepino fruits in the three regions. The main classes of the differentially accumulated metabolites were ranked as Amino acids and derivatives, Nucleotides and derivatives, Organic acids, Alkaloids, Vitamins, Saccharides and Alcohols, Phenolic acids, Lipids, and others. Environmental factor analysis indicated that soil nutrients were the primary differentiating factor. Five soil nutrient indicators: TN（total nitrogen）, TP（total phosphorus）, AP（available phosphorus）, AK（available potassium）, and OM（organic matter）, exhibited significant differences in three growing sites. Metabolite and soil nutrient association analysis using redundancy analysis (RDA) and Mantel test indicated that TNand OM contributed to the accumulation of amino acids and derivatives, nucleotides and derivatives, and alkaloids while inhibiting organic acids, vitamins coagulation biosynthesis. Moreover, AP and TP were associated with the highest accumulation of saccharides and, alcohols, phenolic acids. Consequently, differences in soil nutrients were reflected in Pepino metabolites variability. This study clarified the metabolite variability and the relationship between Pepino and soil nutrients in the main planting areas of northwest China. It provides a theoretical basis for the subsequent development of Pepino's nutritional value and cultivation management.

Mulberries is a type of fruit tree that is rich in nutrients and possesses both medicinal and dietary properties, deeply loved by consumers. The fragrance is a significant factor in the sensory quality of mulberries, playing a crucial role in consumer purchasing behavior. 'Baichang' mulberry is a unique variety of mulberry that emits a strong, creamy-like fragrance, which has enormous potential market value. However, the key metabolites and mechanisms responsible for the formation of this fragrance are still unclear. In this study, we utilized GC-MS technology and RNA-seq to examine the Volatile Organic Compounds (VOCs) and gene expression in 'Baichang' (Morus macroura) mulberries and 'Hongchang' (Morus laevigata) mulberries, the latter of which do not have a distinct fragrance. The results showed that 661 volatile metabolites were detected in both mulberry varieties. Most of these were found in higher relative amounts in the 'Baichang' mulberry variety, with 47 types being present only in the 'Baichang' mulberries, suggesting a rich composition of VOCs in the 'Baichang' mulberry. 312 metabolites were identified as differential metabolites; combining the sensory annotation information and relative content of VOCs, 70 candidate VOCs were annotated as related to the formation of 'sweet, waxy, coconut, and oily' sensations. They could potentially be the key metabolites contributing to the unique aroma of 'Baichang' mulberries. The relative odor activity value (rOAV) analysis revealed that 2(3H)-Furanone, 5-hexyldihydro- was the key VOC contributing to the formation of the special aroma of 'Baichang' mulberries. By RNA-seq, 19 key structural genes related to ester synthesis were identified, including AAT , ACX , ALDH, CYP, EHL, FAD, HPL, and LOX. The high expression of these structural genes in the "Baichang" mulberry fruit is the main reason for its unique creamy aroma. This study provides insights into the aroma differences among different kinds of mulberrie.

Background; Cell-released extracellular vesicles (EVs) acting as 'metabolically and proteolytically active machines,' show potential in metabolomic and proteomic analysis of serum EVs. Despite diverse challenges, post-isolation omics characterization EVs offers crucial insights for effective analysis; (2) Methods: The research, involved children with Congenital Zika Syndrome, utilizing mass spectrometry for proteomics and GC-MS for metabolite identification. Vesicles were isolated using Izon qEV columns, quantified, and characterized by NTA and TEM. Data analysis employed Cytoescape/String and MetaboAnalyst, revealing variations in metabolic and proteomic profiles among groups through PCA and volcano plots. Proteins and Metabolite set enrichment analysis provided biologically meaningful patterns to enriched metabolites; (3) Results: Using molecular exclusion chromatography, the EVs were characterized, revealing size variations. Protein analysis identified 13 significantly altered proteins, including upregulated (e.g., AOM8Q6 - IGLC7) and downregulated (e.g., Q8TD86 - CALML6) ones. Metabolite analysis indicated involvement in the PI3K-AKT-mTOR pathway and suggested a role in Angiotensin inhibition in CZS+. Upstream of mTOR, Akt is the central signaling molecule in the PI3K pathway and plays critical roles in brain development as well as synaptic plasticity important for Zika Virus. The study provides insights into molecular mechanisms associated with CZS; (4) Conclusions: The study pinpointed valuable possible biomarkers, specifically proteins and metabolites, in Zika virus (ZIKV) infection. It stresses the necessity for broader investigations with advanced techniques to uncover molecular targets, potentially advancing pharmacological strategies.

Metabolites are essential intermediate products in metabolism, and metabolism dysregulation indicates different types of diseases. Previous studies have shown that cigarette smoke dysregulated metabolites; however, limited information is available with electronic cigarette (E-cig) vaping. We hypothesized that E-cig vaping and cigarette smoking altered systemic metabolites, and we propose to understand the specific metabolic signature between E-cig users and cigarette smokers. Plasma from non-smoker controls, cigarette smokers, and e-cig users were collected, and metabolites were identified by UPLC–MS (Ultraperformance liquid chromatography-mass spectrometer). Nicotine degradation was activated by e-cig vaping and cigarette smoking with increased concentrations of cotinine, cotinine N-oxide, (S)-nicotine, and (R)-6-hydroxynicotine. Additionly, we found significant decreased concentrations in metabolites associated with tricarboxylic acid (TCA) cycle pathways in e-cig users verses cigarette smokers, such as: D-glucose, (2R,3S)-2,3-dimethylmalate, (R)-2-hydroxyglutarate, O-phosphoethanolamine, malathion, D-threo-isocitrate, malic acid, and 4-acetamidobutanoic acid. Cigarette smoking significant up-regulated sphingolipid metabolites, such as D-sphingosine, ceramide, N-(octadecanoyl)-sphing-4-enine, N-(9Z-octadecenoyl)-sphing-4-enine, and N-[(13Z)-docosenoyl]sphingosine, verses e-cig vaping. Overall, e-cig vaping dysregulated TCA cycle realted metabolites while cigarette smoking altered sphingolipid metabolites. Both e-cig and cigarette smoke increased nicotinic metabolites. Therefore, specific metabolic signature altered by e-cig vaping and cigarette smoking could serve as potential systemic biomarkers for early cardiopulmonary diseases.

Little information is available regarding the impacts of dietary energy level on the gut microbiota and metabolites of donkeys. This studied aimed to explore the effects of dietary energy content on growth performance, intestinal microbiome and metabolome of Dezhou donkeys. Thirty-six 9-month-old male Dezhou donkeys were assigned to two groups fed low or high content energy diets (LE or HE). Results showed that donkeys fed HE had improved (P < 0.05) the average daily gain (ADG) and feed efficiency (G/F), compared with those receiving LE diet. Compared to the LE group, feeding HE specially increased the abundances of unidentified_Prevotellaceae (P = 0.02) while decreased the richness of unidentified_Ruminococcaceae (P = 0.05) of donkeys. Compared to LE group, feeding HE diet significantly (P < 0.05) affected the metabolic pathways involving the aspartate metabolism and urea cycle. In addition, the increased bacteria and metabolites in the HE-fed group exhibited a positive correlation with improved growth performance of donkeys. Taken together, feeding HE diet increased the richness of some specific bacteria and upregulated growth-related metabolic pathways, which contributed to the augmented growth performance of donkeys. Thus, it is a recommendable dietary strategy to feed HE diet to fattening donkey for superior production performance and feed efficiency.

The grain filling rate (GFR) plays a crucial role in determining grain yield. However, the regulatory and molecular mechanism of grain filling rate (GFR) in foxtail millet remains unclear. In this study, we found the GFR of 'Changnong No.47' (CN47) was significantly higher at 14 days after flowering (DAF) and 21 DAF in comparison to 'Changsheng 13' (CS13). Furthermore, CN47 also exhibited higher thousand grain weight and yield than CS13. Therefore, we conducted transcriptomics and metabolomics to analyze the biological processes and functional genes associated with GFR during two stages of grain filling in both cultivars. A total of 765 differentially expressed genes (DEGs) and 246 differentially accumulated metabolites (DAMs) were identified at the 14 DAF stage, while at the 21 DAF stage, a total of 908 DEGs and 268 DAMs were identified. The integrated analysis of co-mapped DAMs and DEGs revealed enriched pathways, including flavonoid biosynthesis, plant hormone signal transduction, tyrosine metabolism, ATP-binding cassette (ABC) transporters, beta-alanine metabolism, as well as stilbenoid, diarylheptanoid and gingerol biosynthesis. In order to elucidate their potential functions in the context of GFR, we developed a gene-metabolite regulatory network for these metabolic pathways. Notably we found some genes associated with ABC transporters and plant hormone signal transduction pathway were implicated in auxin transport and signal transduction, highlighting the crucial role of auxin during grain filling. The results provide initial insights into the regulatory and molecular mechanisms underlying GFR in foxtail millet, as well as offer valuable genetic resources for further elucidation of GFR in future studies. The findings have established a theoretical basis for improving the efficiency of yield breeding in foxtail millet.

Lactobacilli are considered an inexhaustible source of potentially bioactive substances; indeed, several products from their metabolism are known to have immunomodulatory and anti-inflammatory activity. Recently, we demonstrated that cell-free supernatants (CFS) obtained from Lactobacillus (L.) acidophilus, L. plantarum, L. rhamnosus and L. reuteri can impair Candida pathogenic potential in an in vitro model of epithelial vaginal infection. This effect could be ascribed to a direct effect of living lactobacilli on Candida virulence and to the production of metabolites which are able to impair fungal virulence. In the present work, stemming from those data, we deepened our knowledge on the CFS from these 4 lactobacilli by performing a metabolomic analysis to better characterize their composition. By using an untargeted metabolomic approach, we detected consistent differences in the metabolites produced by these four different lactobacilli. Interestingly, L. rhamnosus showed the most peculiar metabolic profile. Specifically, after a hierarchical clustering analysis in positive and negative ionization mode, L. rhamnosus showed a specific area of significant overexpressed metabolites that strongly differed from the same area in other lactobacilli. In this area, inosine was identified among the overexpressed metabolites of L. rhamnosus. This molecule has been described to have antioxidant, anti-inflammatory, anti-infective and neuroprotective properties. The biological significance of its overproduction by L. rhamnosus might be important in its probiotic and/or postbiotic activity.

Tea (Camellia L.) falls into the family Theaceae, is a valuable commercial crop, and tea products made from its buds and young leaves are favored by consumers all over the world. The more common Thea plant is Camellia sinensis (C. sinensis), but its most important relative, Camellia taliensis (C. taliensis), is also utilized by locals in the area of cultivation to manufacture tea. In this investigation, C. taliensis (DL) and C. sinensis (QJZ) were characterized in terms of their agronomic traits, physicochemical indices, metabolomics, and transcriptomics. The leaf area of DL is larger than that of QJZ; the color of DL’s buds and leaves is yellowish-green, while that of QJZ’s is green. DL’s buds and leaves are more densely velvety than those of QJZ. The HPLC results indicated that the physicochemical contents varied considerably between the two samples, with DL having greater concentrations of EGCG and GABA than QJZ, while QJZ had remarkably higher concentrations of C, CA, and EGC than DL. A total of 2269 metabolites and 362,190,414 genes were positively identified, with the number of DAMs and DEGs being 1001 and 34,026, respectively. The flavonoids, phenolic acids, and alkaloid metabolites were dramatically different between the two tea group plants. Bioinformatics profiling revealed that the DAMs and DEGs of the two tea group plants interacted with each other and were involved in metabolic pathways including “biosynthesis of secondary metabolites”, “biosynthesis of amino acids”, “biosynthesis of cofactors”, “phenylpropanoid biosynthesis”, and “flavonoid biosynthesis”. Overall, these results provide statistical support for germplasm conservation and production for both C. taliensis and C. sinensis.

Dairy products are an important source of protein and other nutrients in the Mediterranean diet. In these countries the most common source of milk for producing dairies are cow, goat, sheep and buffalo. Andalusia is traditionally the largest producer of goat milk in Spain. Kefir is a fermented product made from bacteria and yeasts which has health benefits beyond its nutritional properties. There is a lack of knowledge about the molecular mechanisms and metabolites that bring about these benefits. In this work, the combination of analytical techniques (GC-FID, UHPLC-MS-QToF, GC-QqQ-MS, and GC-ToF-MS) resulted in the detection of 105 metabolites in kefir produced with goat milk from two different thermal treatments (raw and pasteurized) fermented at four times (12, 24, 36, and 48 h, using 0 h as control). Of these, 27 metabolites differed between kefir produced with raw and pasteurized milk. These changes could be possibly caused by the effect of pasteurization on the microbial population in the starting milk. Some interesting molecules were identified, as shikimic acid, dehydroabietic acid, GABA and tyramine that could be related to antibacterial properties, enhance of immune system and arterial pressure. Moreover, a viability assay of the NIRS technique was performed to evaluate its use on monitoring the fermentation and classification of samples, which had resulted in a 90 % of correct classified samples according to their fermentation time. This study represents the most comprehensive metabolomic analysis of goat milk kefir so far, revealing the intricate changes in metabolites during fermentation and the impact of milk treatment.

The flowering of Amorphophallus bulbifer plays an important role in its reproduction. The flowers and leaves of A. bulbifer cannot grow at the same time. However, the physiological and molecular mechanisms involved in flower bud and leaf bud formation are still unclear. In this study, the flower buds and leaf buds of A. bulbifer in the early stage of growth were used as research materials, transcriptome and metabolome analyses were carried out, and the soluble sugar and starch contents of A. bulbifer corms were determined. Transcriptome analysis revealed 5 542 differentially expressed genes (DEG) between flower buds and leaf buds, 3 107 of which were upregulated and 2 435 of which were downregulated. Enrichment analysis of the KEGG pathway showed that these differential genes were enriched mainly in the plant hormone signal transduction, DNA replication and fatty acid elongation pathways. Plant hormone signal transduction, DNA replication and fatty acid elongation pathways. A total of 5 296 significant differentially abundant metabolites were screened out by nontargeted metabolomics analysis. The differentially abundant metabolites were functionally classified in the HMDB, and 118 were successfully matched, including 17 that were highly expressed in flower buds. The differentially abundant metabolites in the flower buds were mainly enriched in pathways such as amino acid metabolism, isoquinoline alkaloid biosynthesis and pyrimidine metabolism. Targeted metabolomics analysis revealed that the contents of ABA, ZT and iPA in flower buds were significantly greater than those in leaf buds, while the opposite trend was observed for IAA. The analysis of soluble sugar and starch contents showed that the starch and soluble sugar contents in flower buds were significantly greater than those in leaf buds. The results of this study showed that flower bud development in A. bulbifer was regulated by amino acids, starch, ABA, ZT, iPA, IAA and other hormones. These findings could lead to valuable genetic resources for further study of A. bulbifer flowering and provide a deeper understanding of the molecular basis of A. bulbifer flowering.

Basil, renowned for its aromatic properties, exhibits commendable drought tolerance and holds significant value both as an edible and medicinal plant. Recognizing the scarcity of studies addressing basil’s response to drought stress, we undertook a comprehensive analysis of the volatile metabolome and transcriptome of sweet basil across four distinct levels of drought stress. Our metabolic analysis meticulously identified 830 metabolites, with 215 differentially accumulated metabolites discerned. Notably, the primary constituents of sweet basil volatiles exhibited minimal alterations, while the differentially accumulated metabolites were predominantly lipids and terpenes. The transcriptome analysis unveiled 27,181 differentially expressed DEGs, with a predominant focus on metabolic pathways and biosynthesis of secondary metabolites. Integrating insights from both transcriptome and volatile metabolomic analyses highlighted the pivotal roles of Alpha-linolenic acid, flavonoid, and lignin metabolism in fortifying the resistance of sweet basil against drought stress. This holistic approach not only enriches our understanding of the molecular intricacies underpinning basil’s drought resistance but also furnishes valuable insights for the molecular breeding of basil varieties endowed with enhanced drought tolerance.

Aspergillus montevidensis is an important domesticated fungus that has been applied to produce many traditional fermented foods under high osmotic conditions. However, the detailed mechanisms of tolerance to osmotic stress remain largely unknown. Here, we construct a target-deleted strain (ΔLeuRS) of A. montevidensis and found that the ΔLeuRS mutants grew slowly and suppressed the development of the cleistothecium compared to the wide-type strains (WT) under salt-stressed conditions. Furthermore, differentially expressed genes (P<0.0001) governed by LeuRS were involved in salt tolerance, ABC transporter, amino acid metabolism, sugar metabolism, and reproduction process. The ΔLeuRS strains compared to WT strains under short- and long-term salinity stress especially altered accumulation levels of metabolites, such as amino acids and derivatives, carbohydrates, organic acids, and fatty acids. The study provides new insights into the underlying mechanisms of salinity tolerance and lays a foundation for favor improvement of foods fermented with A. montevidensis.

Autophagy is an evolutionarily conserved mechanism for degrading and recycling different cellular components in both normal development and stress conditions. Our recent research demonstrated that autophagy-mediated compartmental cytoplasmic deletion is essential for pollen germination. However, how autophagy regulates pollen germination to ensure its fertility remains largely unknown. Here, we applied multi-omic analyses to investigate the downstream pathways of autophagy in the process of pollen germination. Although ATG2 and ATG5 play similar roles in regulating pollen germination, high-throughput transcriptomic analysis reveals that silencing ATG5 has greater impact on the transcriptome than silencing ATG2. Cross-comparisons of transcriptome and proteome analysis reveal that gene expression at mRNA level and protein level are differentially affected by autophagy. Furthermore, high-throughput metabolomics analysis demonstrates that pathways related amino acid metabolism and aminoacyl-tRNA biosynthesis can be affected by both ATG2 and ATG5 silencing. Collectively, our multi-omic analyses reveal a central role of autophagy in cellular metabolism, which is critical for the initiation of pollen germination and the guarantee of pollen fertility.

Muscle mass, strength and physical function are known to decline with age. This is associated with the development of geriatric syndromes including sarcopenia and frailty. These conditions are associated with disability, falls, longer hospital stay, higher readmission rates, institutionalisation, osteoporosis, and death. Moreover, they are associated with reduced quality of life, as well as substantial costs to health services around the world. Dietary protein is essential for skeletal muscle function. Older adults have shown evidence of anabolic resistance, where greater amounts of protein are required to stimulate muscle protein synthesis and therefore require higher daily amounts of dietary protein. Research shows that resistance exercise has the most beneficial effect on preserving skeletal muscle. A synergistic effect has been noted when this is combined with dietary protein, yet studies in this area lack consistency. This is due, in part, to the variation that exists within dietary protein, in terms of dose, quality, source, amino acid composition and timing. Research has targeted participants that are replete in dietary protein with negative results. Inconsistent measures of muscle mass, muscle function, physical activity and diet are used. This review attempts to summarise these issues, as well as introduce the possible role of the gut microbiome and its metabolome in this area.

Chinese pepper rust is a live parasitic fungal disease caused by Coleosporium zanthoxyli, which seriously affects the cultivation and industrial development of Z. armatum. Cultivating and planting resistant cultivars is considered the most economical and environmentally friendly strategy to control this disease. Therefore, the mining of excellent genes for rust resistance and analysis of the mechanism of rust resistance are the key strategies to achieve the targeted breeding of rust resistance. However, there is no relevant report on pepper rust resistance at present. The aim of the present study was to further explore the resistance mechanism of pepper by screening the rust-resistant germplasm resources in the early stage. Combined with the analysis of plant pathology, transcriptomics, and metabolomics, we found that the genes and metabolites related to phenylpropanoid metabolism were highly enriched in resistant varieties after pathogen infection, which indicated that phenylpropanoid metabolism might mediate the resistance of Z. armatum. This finding was further confirmed by real-time quantitative polymerase chain reaction analysis, which revealed that the expression levels of core genes involved in phenylpropane metabolism in disease-resistant varieties were high. In addition, the difference in flavonoid content in the leaves between resistant and susceptible varieties further supported the conclusion that the flavonoid pathway is one of the main pathways involved in resistance formation in Chinese pepper, and MeJA is involved in the formation of resistance. Our research results not only help to better understand the resistance mechanism of Z. armatum rust but also contribute to the breeding and utilization of resistant varieties.

The gut microbiota plays an important role in the physiological activities of the host and affects the formation of important economic traits in agricultural animals. We investigated the effects of cecal microbiota on chicken weights using the Guizhou yellow chicken as a model. We collected experimental cohorts from chickens with high (HC, n=16) and low body weights (LC, n=16) and integrated microbial 16S rRNA gene sequencing and non-targeted serum metabolome data to explore the effect and its metabolic mechanism of cecal microbiota on market weight. The genera Lachnoclostridium, Alistipes, Negativibacillus, Sellimonas and Ruminococcus torques group were enriched in the HC group while Phascolarctobacterium was enriched in the LC group (P<0.05). Metabolomic analysis determined that pantothenic acid, luvangetin (2H-1-benzopyran-6-acrylic acid) and menadione (vitamin K) were significantly higher in HC serum while beclomethasone dipropionate (a glucocorticoid) and chlorophene (2-benzyl-4-chlorophenol) were present at higher levels in the LC group. The microbes enriched in HC that were significantly positively correlated with metabolites including pantothenic acid and menadione and negatively correlated with beclomethasone dipropionate and chlorophene. These results indicated that specific cecal bacteria in Guizhou yellow chickens alter the host metabolism and growth performance. This study provides a reference for revealing the mechanism of cecal microbe actions that affect chicken body weight.

The development of pre-hierarchical follicle (PHF), especially small yellow follicles (SYFs), directly affects the recruitment of dominant follicles and thus affects the egg-laying performance of chickens. However, the development of PHF, especially the development of SYF, and its regulatory mechanism remain unclear. Therefore, we performed transcriptomic and metabolomic analyses of large white follicles (LWFs) and SYFs in chickens. Transcriptome sequencing revealed 258 differentially expressed genes (DEGs) between SYF and LWF, of which 172 were upregulated and 86 were downregulated. The DEGs were mapped to 17 KEGG pathways, mainly the gap junction, calcium signaling, and neuroactive ligand-receptor interaction pathways. The results of the metabolome analysis revealed 129 significant differential metabolites (DMs), including 36 upregulated DMs and 93 downregulated DMs. The DMs were mapped to 9 KEGG pathways for follicle tissue, which included mainly glutathione metabolism, alpha-linolenic acid metabolism, and tryptophan metabolism, etc. The combined transcriptional and metabolic analysis revealed significantly enriched pathways, and four metabolically related pathways, including glutathione metabolism, alpha-linolenic acid metabolism, linoleic acid metabolism, and pyrimidine metabolism, were identified. Glutathione metabolism is a critical signaling pathway that may affect ovarian follicle development to regulate the SYF reserve process in chickens. These results can act as a reference for improving the egg-laying performance of Tengchong snow chickens.

Despite substantial evidence supporting the efficacy of prebiotics for promoting host health and stress resilience, few experiments present evidence documenting the dynamic changes in microbial ecology and fecal microbial-modified metabolites across time. Furthermore, the literature reports a lack of reproducible effects of prebiotics on specific bacteria and bacterial-modified metabolites. The current experiments examined whether consumption of diets enriched in prebiotics (galactooligosaccharides, GOS and polydextrose, PDX) compared to control diet, would consistently impact the gut microbiome and microbial-modified bile acids across time and between two research sites. Male Sprague Dawley rats were fed control or prebiotic diets for several weeks, and their gut microbiome and metabolome were examined using 16S rRNA gene sequencing and untargeted LC-MS/MS analysis. Dietary prebiotics altered beta diversity, relative abundances of bacterial genera, and microbially modified bile acids across time. PICRUSt2 analyses identified four inferred functional metabolic pathways modified by prebiotic diet. Correlational network analyses between inferred metabolic pathways and microbial-modified bile acids revealed deoxycholic acid as a potential network hub. All these reported effects were consistent between the two research sites supporting the conclusion that dietary prebiotics robustly changed the gut microbial ecosystem. Consistent with our previous work demonstrating that GOS/PDX reduces the negative impacts of stressor exposure, we propose that ingesting a diet enriched in prebiotics facilitates the development of a health-promoting gut microbial ecosystem.

Despite substantial heterogeneity of studies, there is evidence that antibiotics commonly used in primary care influence the composition of the gastrointestinal microbiota in terms of changing the composition and/or diversity. Benzyl isothiocyanate (BITC) from the food and medicinal plant nasturtium (Tropaeolum majus) is known for its antimicrobial activity and is used for the treatment against infections of the draining urinary tract and upper respiratory tract. Against this background, we raised the question whether 14 d nasturtium intervention (3 g daily, N=30 healthy females) could also impact the normal gut microbiota composition. Spot urinary BITC excretion highly correlated with a weak, but significant antibacterial effect against Escherichia coli. A significant increase in human beta defensin 1 as parameter for host defense was seen in urine and exhaled breath condensate (EBC) upon verum intervention. Pre-to-post analysis revealed that mean gut microbiome composition did not significantly differ between groups, nor did circulating serum metabolome. On an individual level, partly large changes were observed between sampling points, though. Explorative Spearman rank correlation analysis in subgroups revealed associations between gut microbiota and the circulating metabolome, as well as between changes in blood markers and bacterial gut species.

Pregnancy is a dynamic state with multiple metabolic changes occurring including insulin resistance. Gestational diabetes mellitus (GDM), a form of diabetes that appears during pregnancy, develops if metabolic aberrations occur, in particular, in normal pregnancy-induced insulin resistance. Multi-omics is a powerful approach for uncovering the mechanisms driving metabolic change in different physiologic and pathologic states. A recent study demonstrated that the gestational gut microbiome mediates pregnancy metabolic adaptations through effects on gut indoleamine-2,3 dioxygenase 1 activity and the production of kynurenine. Using the dataset generated from this highly controlled study, we performed a comprehensive analysis of the pregnancy-specific physiological and metabolic profiles, 16S rRNA microbiome, and plasma untargeted LC-MS metabolome data. To facilitate the utilization of these analysis results by other researchers, we developed MOMMI-MP, a database that provides an easy-to-use platform to browse and search differential abundant microbial taxa and metabolites, and to examine metabolic pathways. The datasets consist of data collected from 3 genetically diverse strains of mice (C57BL/6J, CD1, and NIH-Swiss) over 6 time points during the gestational (days 0, 10, 15, and 19 during gestation) and postpartum (days 3 and 20 after delivery) states, totaling 180 samples for each strain. The computational results are presented in various tables and plots, and organized in MOMMI-MP to empower exploratory analyses by other researchers. In conclusion, MOMMI-MP is a resource to facilitate the investigation of novel mechanisms governing metabolic changes during pregnancy.

Inflammatory bowel disease (IBD) is an incurable, chronic disorder of the gastrointestinal tract, whose incidence increases every year. Scientific research is constantly delivering new information about the disease and its multivariate, complex etiology. Nevertheless, full discovery and understanding of the complete mechanism of IBD pathogenesis still pose a significant challenge to today's science. Recent studies unanimously confirmed the association of gut microbial dysbiosis with IBD, as well as its contribution to the regulation of the inflammatory process. It transpires that not only the altered composition of pathogenic and commensal bacteria is characteristic of disturbed intestinal homeostasis in IBD, but also of viruses, parasites, and fungi, which are active in the intestine. In fact, the crucial function of microbial metabolome in the human body is altered, which causes a wide range of effects in the host, thus providing a basis for the disease. On the other hand, human genomic and functional research revealed more loci that play an essential role in gut homeostasis regulation, immune response, and intestinal epithelial function. This review aims to organize and summarize currently available knowledge concerning the role and interaction of crucial factors associated with IBD pathogenesis, particularly host genetic composition, intestinal microbiota, and metabolome, with immune regulation.

Chinese Taihe Black-bone silky fowl (TBsf) is the homology of medicine and food and has high nutritional and medical value all over the world. However, the nutritional compositions and specific metabolite advantages of Taihe silky fowl muscle are still poorly understood. In this study, we investigated the differences of nutritional components between TBsf and another similar breed (Black Feathered chicken and laid green-shelled eggs, BF-gsc). Meanwhile, we also explored the divergences in muscle characteristics of Taihe silky fowl fed with two different diets, that is normal chicken feed (TBsf-ncf) and Broussonetia papyrifera-fermented feed (TBsf-bpf). Firstly, the growth performance and biochemical index of Taihe silky fowl was significantly different compared with black-feathered chicken. Secondly, we identified the metabolic alterations in Taihe silky fowl by performing an un-targeted UHPLC-Q-TOF-MS/MS analysis. Our results suggested that the whole metabonomic characteristics had obvious separation between TBsf-ncf, TBsf-bpf and BF-gsc groups both in the positive and negative ion mode by PCA analysis. Next, OPLS-DA multivariate analysis revealed that 57 metabolites (in positive mode) and 49 metabolites (in negative mode) were identified as differential metabolites between TBsf-ncf and BF-gsc group. These differential metabolites were mainly enriched to ABC transporters, biosynthesis of amino acids and aminoacyl-tRNA biosynthesis. Besides, there were 47 metabolites (in positive) and 13 metabolites (in negative) were differentially regulated between TBsf-ncf and TBsf-bpf group, which were majorly involved in histidine metabolism and linoleic metabolism. Furthermore, the integrated network analysis suggested that DL-arginine, DL-isoleucine, linoleoylcarnitine, stearoylcarnitine (positive) and ricionleic acid, D-proline, uric acid (negative) were the significantly metabolic biomarkers in Taihe silky fowl. Moreover, the metabolites of primaquine, ticlpoidine, riboflavin, acetylcarnitine (positive) and salicylic acid, acetaminophen sulfate, glutamic acid (negative) were markedly changed in the Taihe silky fowl fed with BP-fermented feed. In summary, a global survey of the nutritional components and metabolite differences were performed in muscle tissues of Taihe silky fowl between various breeds and feeds. The comprehensive expression profiles of the metabolites in Taihe silky fowl affected by genetic and environmental factors were acquired. This study provided valuable evidence fo breed and feed-induced putative biomarkers as well as improved the economic value of Taihe silky fowl through targeted metabolite regulation.

Maternal obesity and gestational diabetes mellitus (GDM) are linked with impaired placental function and early onset of non-communicable cardiometabolic diseases in offspring. Previous studies have highlighted that the dietary non-esterified fatty acids (NEFAs), palmitate (PA) and oleate (OA), key dietary metabolites associated with maternal obesity and GDM, are potential modulators of placental lipid processing. Using the BeWo cell line model, the current study integrated transcriptomic (mRNA microarray), metabolomic, and lipidomic readouts to characterize the underlying impacts of exogenous PA and OA on placental villous trophoblast cell metabolism. Targeted gas chromatography and thin layer chromatography highlighted that saturated and monounsaturated NEFAs differentially impact BeWo cell lipid profiles. Furthermore, cellular lipid profiles differed when exposed to single and multiple NEFA species. Additional multi-omic analyses suggested that PA exposure is associated with enrichment in β-oxidation pathways, while OA exposure is associated with enrichment in anti-inflammatory and antioxidant pathways. Overall, this study further demonstrated that dietary PA and OA are important regulators of placental lipid metabolism. Encouraging appropriate dietary advise and implementing dietary interventions that maintain appropriate placental function by limiting excessive exposure to saturated NEFAs such as PA, will continue to be crucial in the clinical management of at-risk obese and GDM pregnancies.