Gut microbiome pattern impacts treatment response in primary biliary cholangitis.

BACKGROUND: Primary biliary cholangitis (PBC) is a progressive autoimmune liver disease. An inadequate response to ursodeoxycholic acid (UDCA) poses a high risk of progression toward end-stage liver disease. Gut dysbiosis has been implicated in PBC. Here, we aimed to investigate microbial signatures that permit risk stratification and provide mechanistic insights into novel therapies for PBC. METHODS: We prospectively recruited UDCA treatment-naive patients with PBC and performed metagenomic sequencing and metabolomic profiling using stool and serum samples obtained before (n = 132) and after (n = 59) treatment. PBC microbiome subtypes were identified using unsupervised machine learning methods and validated in two independent cohorts. FINDINGS: PBC baseline metagenomes clustered into two community subtypes characterized by varying abundances of Clostridia taxa. Compared with Clostridialow microbiomes, Clostridiahigh microbiomes were more similar to healthy controls. Notably, patients in the Clostridialow subtype exhibited a 2-fold higher UDCA non-response rate compared to those in the Clostridiahigh subtype (41% vs. 20%, p = 0.015). Integrative analysis of metagenomic and metabolomic data revealed divergent functional modules and metabolic activities between the two metacommunities. In particular, anaerobic fermentation and the production of bioactive metabolites, including tryptophan derivatives and secondary bile acids, crucial for immune regulation and gut barrier maintenance, were markedly diminished in the Clostridialow subtype. Moreover, UDCA administration reconfigured the fecal microbial and metabolic profiles only in the Clostridiahigh group. Importantly, the microbiome subtypes and their associations with UDCA response were reproducible in two independent treatment-naive PBC cohorts. CONCLUSIONS: Characterizing baseline microbiota patterns may enable the prediction of treatment outcomes in PBC and facilitate personalized treatment strategies. FUNDING: This research was mainly supported by the National Natural Science Foundation of China.

Optimizing Skin Surface Metabolomics: A Comprehensive Evaluation of Sampling Methods, Extraction Solvents, and Analytical Techniques.

Characterizing the metabolite fingerprint from the skin surface provides invaluable insights into skin biology and microbe-host interactions. To ensure data accuracy and reproducibility, it is essential to develop standard operating procedures (SOPs) for skin surface metabolomics. However, there is a notable lack of studies in this area. Here, we thoroughly evaluated different sampling materials, extraction solvents, taping methods (frequency and number of tapes) and analytical techniques to optimize skin surface metabolomics. Our results showed that the combination of D-Squame® D100 tape with a methyl tert-butyl ether/methanol extractant is optimal for skin surface lipidomics. Performing the skin taping procedure five times with one tape yields sufficient biomass for lipid analysis, while the optimal taping procedure varies for water-soluble compounds. In addition, our study identified associations among the skin surface metabolites, some of which potentially underlie the formation of microbial cutotypes and offer insights into host-microbe interactions.

Effects of inactivated Lactobacillus rhamnosus on growth performance, serum indicators, and colonic microbiota and metabolism of weaned piglets.

BACKGROUND: To assess the effects of inactivated Lactobacillus rhamnosus (ILR) on growth performance, serum biochemical indices, colonic microbiota, and metabolomics in weaned piglets, 120 piglets were randomly divided into five groups. Samples in the control group were fed a basal diet, while the experimental ILR1, ILR2, ILR3, and ILR4 groups were fed basal diets supplemented with 0.1%, 0.2%, 0.3%, and 0.4% ILR, respectively. The prefeeding period lasted for 5 days and was followed by a formal period of 28 days. RESULTS: Compared to the control, the average daily gain increased by 4.38%, 7.98%, 19.32%, and 18.80% for ILR1, ILR2, ILR3, and ILR4, respectively, and the ratio of feed to gain decreased by 0.63%, 3.80%, 12.66%, and 10.76%, respectively. Serum IgA, IgG, IgM, total antioxidant capacity, and glutathione peroxidase levels increased significantly in weaned piglets in the treatment groups. Addition of 0.3% ILR significantly increased the Shannon and Simpson indices of the colonic microbiota in weaned piglets and altered the microbiota composition. Changes in metabolic profiles were observed and were primarily related to the urea cycle, amino acid metabolism, and lipid metabolism. CONCLUSION: ILR improved growth performance and serum immunological and biochemical indices and optimized the colonic microbiota structure and metabolism of weaned piglets.

Characteristics of the Serum Microbiota and Circulating Metabolites in Cynomolgus Monkeys With Spontaneous Type 2 Diabetes Mellitus.

BACKGROUND: Type 2 diabetes mellitus (T2DM) is widely recognized as a serious global public health concern with a substantial economic burden on patients, their families, and society. Accumulating evidence suggests that an etiologic role for serum microbiota and circulating metabolites in the pathogenesis of T2DM. This study aims to characterize the serum microbiota and circulating metabolites in cynomolgus monkeys with spontaneous T2DM, and provide a reference for the diagnosis and treatment of clinical T2DM. METHODS: We collected serum samples of the 14 cynomolgus monkeys (15-20 years old, male) for serum microbiota analysis by 16S rRNA gene V3-V4 region amplicon sequencing and circulating metabolites analysis by ultra-high-performance liquid chromatography-tandem mass spectrometry, of which seven were spontaneous T2DM cynomolgus monkeys and seven were healthy controls. RESULTS: Our results showed that the serum microbiota abundance and diversity were significantly increased in cynomolgus monkeys with spontaneous T2DM compared to healthy controls, the phyla of Cyanobacteria and Chloroflexi and the genera of Lactobacillus, rhodobacter and collinsella were also significantly increased. A total of 114 serum differentially expressed metabolites (DEMs) were identified, of which 22 were selected as potential biomarkers candidates related to spontaneous T2DM in cynomolgus monkeys by multivariate data analysis. In addition, serum levels of total SCFAs, acetate, butyrate, caproate, isobutyrate, and isovalerate were also significantly increased in the present study. The correlation network analyses have selected certain key DEMs, such as D-Psicose, 4-Oxoproline, D-Glutamine, and Hydroxyphenyllactic acid, which may serve as potential biomarkers for distinguishing between T2DM and healthy controls. CONCLUSION: Our results provide preliminary insights on perturbed serum microbiota and circulating metabolites of cynomolgus monkeys with spontaneous T2DM. These findings would be useful to develop microbiota-based strategies for T2DM prevention and control.

Early Postmortem Beef Muscle Proteome and Metabolome Variations Due to Supranutritional Zinc and Ractopamine Hydrochloride Supplementation.

It was hypothesized that the longissimus thoracis (LT) muscle proteome, phosphoproteome, and metabolome could explain postmortem metabolism and tenderness differences in muscle from cattle supplemented zinc (Zn) and/or ractopamine hydrochloride (RH). High percentage Angus steers (N=20) were fed in a 2x2 factorial assigned to Zn and RH treatments: control (CON; n=10; analyzed 36 mg Zn/kg dry matter [DM]) or supranutritional Zn supplementation (SUPZN; n=10; control diet + 60 mg Zn/kg DM [from ZnSO4] + 60 mg Zn/kg DM [from Zn-amino acid complex]) for the entire 89-d trial. During the 28 d before harvest, steers were blocked by body weight within Zn treatments to RH treatments of 0 (NO; n=10) or 300 mg (RAC; n=10) per steer per day. Steers were harvested at the Iowa State Meat Laboratory, where pH decline (1, 3, 6, and 24 h postmortem) was measured. At 24 h postmortem, LT muscle sections were removed from carcasses, and steaks were analyzed for Warner-Bratzler shear force (WBSF) values at 1, 3, 7, and 14 d postmortem. Muscle samples were taken at 1 h, 1, 3, 7, and 14 d postmortem for the following analysis: troponin-T degradation (1, 3, 7, and 14 d postmortem), myosin heavy chain (MHC) analysis (1 h postmortem), sarcoplasmic proteome analysis through tandem mass tagging analysis (TMT; 1 h and 1 d postmortem), metabolome analysis (1 h and 1 d postmortem), and phosphoproteome analysis (1 h postmortem). SUPZN-NO tended to have a lower (P=0.06) pH at 6 h postmortem and a lower WBSF value (P=0.06) at 1 d postmortem. CON-RAC had a higher (P=0.04) pH at 6 h postmortem and WBSF value (P<0.01) at 1 d postmortem. A lower pH at 6 h postmortem and lower WBSF value at 1 d postmortem in the SUPZN-NO treatment was accompanied by more sorbitol and fructose at 1 d postmortem, and less myosin regulatory light chain 2 at 1 h postmortem, and less adenosine monophosphate deaminase 1 (AMPD1) at 1 d postmortem than all other treatments. A higher pH at 6 h postmortem and higher WBSF value at 1 d postmortem in CON-RAC and SUPZN-RAC was accompanied by more soluble structural proteins (troponin-T and myosin-7) at 1 h postmortem than CON-NO. At 1 h postmortem, CON-RAC had more glyceraldehyde-3-phosphate dehydrogenase than CON-NO or SUPZN-RAC. Differences in energy metabolism enzymes, metabolites, and structural proteins may affect ATP production, rigor development, and lactate buildup which may explain the differences in postmortem metabolism and tenderness development at 1 d postmortem.

Characterization of volatile aroma compounds in pak choi.

Aroma is a key sensory factor in the flavor evaluation of pak choi (Brassica rapa L. ssp. chinensis var. Makino). The pak choi varieties Xiangqingcai (XQC) and Xiuhuajin (XHJ) have unique aroma characteristics, but the chemical profiles of these aromas are unknown. Here, the aroma profiles of three varieties of pak choi including XQC, XHJ, and Suzhouqing (CK, non-aromatic) were determined using gas chromatography-mass spectrometry (GC-MS) and relative odor activity values (rOAV). A total of 15 categories of 716 volatile metabolites were detected in the three pak choi varieties, with terpenoid metabolites identified as the major components, although in each sample the identity of the major terpenoid metabolite varied. There were 53 aroma components in XQC and 54 aroma components in XHJ with rOAV >1, which contribute to rice aroma and fishy odor of these varieties, respectively.

Gut microbiome and metabolome profiling in coal workers' pneumoconiosis: potential links to pulmonary function.

Coal workers' pneumoconiosis (CWP) is a severe occupational disease resulting from prolonged exposure to coal dust. However, its pathogenesis remains elusive, compounded by a lack of early detection markers and effective treatments. Although the impact of gut microbiota on lung diseases is acknowledged, its specific role in CWP is unclear. This study aims to explore changes in the gut microbiome and metabolome in CWP, while also assessing the correlation between gut microbes and alterations in lung function. Fecal specimens from 43 CWP patients and 48 dust-exposed workers (DEW) were examined using 16S rRNA gene sequencing for microbiota and liquid chromatography-mass spectrometry for metabolite profiling. We observed similar gut microbial α-diversity but significant differences in flora composition (ß-diversity) between patients with CWP and the DEW group. After adjusting for age using multifactorial linear regression analysis (MaAsLin2), the distinct gut microbiome profile in CWP patients revealed an increased presence of pro-inflammatory microorganisms such as Klebsiella and Haemophilus. Furthermore, in CWP patients, alterations in gut microbiota-particularly reduced α-diversity and changes in microbial composition-were significantly correlated with impaired pulmonary function, a relationship not observed in DEW. This underscores the specific impact of gut microbiota on pulmonary health in individuals with CWP. Metabolomic analysis of fecal samples from CWP patients and DEW identified 218 differential metabolites between the two groups, with a predominant increase in metabolites in CWP patients, suggesting enhanced metabolic activity in CWP. Key altered metabolites included various lipids, amino acids, and organic compounds, with silibinin emerging as a potential biomarker. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis linked these metabolites to pathways relevant to the development of pulmonary fibrosis. Additionally, studies on the interaction between microbiota and metabolites showed positive correlations between certain bacteria and increased metabolites in CWP, further elucidating the complex interplay in this disease state. Our findings suggest a potential contributory role of gut microbiota in CWP pathogenesis through metabolic regulation, with implications for diagnostic biomarkers and understanding disease mechanisms, warranting further molecular investigation. IMPORTANCE: The findings have significant implications for the early diagnosis and treatment of coal workers' pneumoconiosis, highlighting the potential of gut microbiota as diagnostic biomarkers. They pave the way for new research into gut microbiota-based therapeutic strategies, potentially focusing on modifying gut microbiota to mitigate disease progression.

Responses of Brassica napus to soil cadmium under elevated CO2 concentration based on rhizosphere microbiome, root transcriptome and metabolome.

Rising atmospheric carbon dioxide (CO2) and soil heavy metal pollution affect crop safety and production. Exposure to elevated CO2 (ECO2) increases cadmium (Cd) uptake in some crops like wheat and rice, however, it remains unclear how ECO2 affects Cd uptake by Brassica napus. Here, we investigated the responses of B. napus seedlings exposed to ECO2 and Cd through analyses of physiology, transcriptome, metabolome, and rhizosphere microbes. Compared with Cd-stress alone (Cd50_ACO2), ECO2 boosted the uptake of Cd by B. napus roots by 38.78% under coupled stresses (Cd50_ECO2). The biomass and leaf chlorophyll a content increased by 38.49% and 79.66% respectively in Cd50_ECO2 relative to Cd50_ACO2. Activities of superoxide dismutase (SOD) and peroxidase (POD) enhanced by 8.42% and 185.01%, respectively, while glutathione (GSH) and ascorbic acid (AsA) contents increased by 16.44% and 52.48%, and abundances of rhizosphere microbes changed significantly under coupled stresses (Cd50_ECO2) relative to Cd-stress alone (Cd50_ACO2). Also, the upregulation of glutathione, glutathione transferase genes, and heavy metal ATPase expression promoted the detoxification effect of rapeseed on Cd. Changes in the expression of transcription factors like MAPK, WRKY, BAK1 and PR1, as well as changes in metabolic pathways like ß-alanine, may be involved in the regulatory mechanism of stress response. These findings provide new insights for studying the regulatory mechanism of rapeseed under ECO2 on soil Cd stress, and also provide a basis for further research on Cd tolerant rapeseed varieties in the future climate context.

Revealing the aromatic sonata through terpenoid profiling and gene expression analysis of aromatic and non-aromatic coconut varieties.

Aromatic coconut represents an exceptional variety of coconut known for its distinct and delightful flavor and aroma, both of which are highly cherished by consumers. Despite its popularity, there has been a lack of systematic research on aroma components and the associated synthetic genes. In this report, we developed the metabolite profiles of terpenoids by targeted metabolomics and obtained the expression profile of genes related to terpenoid biosynthesis by RNA-seq during different coconut fruit developmental stages. Totally, we separated 26 different terpenoids in aromatic coconut pulp, among which, geranyl acetate and (-)-isosyngene emerged as the most abundant. The integrated analysis of metabolism and RNA-seq data showed that HMGS2, HMGS3, IPI/IDI1, HMGR1, HMGR3, and CMK2 as potentially key genes involved in the synthesis of terpenoids in aromatic coconut. To validate these findings, qRT-PCR was conducted on terpenoid-related genes. These findings lay a foundation for understanding aroma formation and the molecular mechanism of terpenoids in coconut fruit.

Integrative analysis of transcriptome and metabolome reveals how ethylene increases natural rubber yield in Hevea brasiliensis.

Hevea brasiliensis is an important cash crop with the product named natural rubber (NR) for markets. Ethylene (ET) is the most effective yield stimulant in NR production but the molecular mechanism remains incomplete. Here, latex properties analysis, transcriptome analysis, and metabolic profiling were performed to investigate the mechanism of NR yield increase in four consecutive tappings after ET stimulation. The results revealed that sucrose and inorganic phosphate content correlated positively with dry-rubber yield and were induced upon ET stimulation. Stimulation with ET also led to significant changes in gene expression and metabolite content. Genes involved in phytohormone biosynthesis and general signal transduction as well as 51 transcription factors potentially involved in the ET response were also identified. Additionally, KEGG annotation of differentially accumulated metabolites suggested that metabolites involved in secondary metabolites, amino-acid biosynthesis, ABC transporters, and galactose metabolism were accumulated in response to ET. Integrative analysis of the data collected by transcriptomics and metabolomics identified those differentially expressed genes and differentially accumulated metabolites are mainly involved in amino-acid biosynthesis and carbohydrate metabolism. Correlation analysis of genes and metabolites showed a strong correlation between amino-acid biosynthesis during ET stimulation. These findings provide new insights into the molecular mechanism underlying the ET-induced increase in rubber yield and further our understanding of the regulatory mechanism of ethylene signaling in rubber biosynthesis.

Potassium indole-3-butyric acid affects rice's adaptability to salt stress by regulating carbon metabolism, transcription factor genes expression, and biosynthesis of secondary metabolites.

Soil salinity pollution is increasing worldwide, seriously affecting plant growth and crop production. Existing reports on how potassium indole-3-butyric acid (IBAK) regulates rice salt stress adaptation by affecting rice carbon metabolism, transcription factor (TF) genes expression, and biosynthesis of secondary metabolites still have limitations. In this study, an IBAK solution at 40 mg L-1 was sprayed on rice leaves at the seedling stage. The results showed that the IBAK application could promote shoot and root growth, decrease sucrose and fructose content, increase starch content, and enhance acid invertase (AI) and neutral invertase (NI) activity under salt stress, indicating altered carbon allocation. Furthermore, the expression of TF genes belonging to the ethylene responsive factor (ERF), WRKY, and basic helix-loop-helix (bHLH) families was influenced by IBAK. Many key genes (OsSSIIc, OsSHM1, and OsPPDKB) and metabolites (2-oxoglutaric acid, fumaric acid, and succinic acid) were upregulated in the carbon metabolism pathway. In addition, this study highlighted the role of IBAK in regulating the biosynthesis of secondary metabolites pathway, potentially contributing to rice stress adaptability. The results of this study can provide new sustainable development solutions for agricultural production.

Genome assembly of Stephania longa provides insight into cepharanthine biosynthesis.

Introduction: Stephania longa, a medicinal plant renowned for producing cepharanthine, has gained significance due to the compound's notable antiviral properties against SARS-CoV-2. However, a comprehensive genetic understanding of S. longa has been lacking. This study aimed to develop a high-quality, chromosome-level genome assembly to uncover the genetic intricacies and evolutionary narrative of this species. By integrating genomic data with metabolomic and transcriptomic analyses, we sought to identify key genes involved in cepharanthine biosynthesis. Methods: We employed a multi-faceted approach comprising genome assembly, phylogenetic analysis, gene family dynamics investigation, metabolomic profiling, and gene expression analysis across various tissues of S. longa. This integrated strategy enabled the identification of key genes involved in cepharanthine biosynthesis and elucidated the species' evolutionary history. Results: Our phylogenetic analysis clarified the placement of the genus Stephania within the Ranunculales order and revealed its notably high mutation rate. We identified gene family expansions and signs of positive selection likely contributing to Stephania's unique metabolic capabilities. Metabolomic profiling uncovered complex regulatory mechanisms orchestrating the biosynthesis and distribution of cepharanthine and related metabolites. Through the integration of genomic, transcriptomic, and metabolomic data, we identified genes with expression patterns and evolutionary trajectories suggesting pivotal roles in cepharanthine biosynthesis, including those involved in crucial biosynthetic steps. Discussion: This comprehensive study, integrating genomic, metabolomic, and transcriptomic approaches, provides valuable insights into S. longa's biosynthetic potential. It not only enhances our understanding of the species but also establishes a foundation for future investigations into the biosynthesis and therapeutic exploitation of cepharanthine and related alkaloids.

Metabolomic Analysis of Carotenoids Biosynthesis by Sphingopyxis sp. USTB-05.

Carotenoids belonging to the class of tetraterpenoids have extensive applications in medicine, food, nutrition, cosmetics, and feed. Among them, lutein and zeaxanthin can prevent macular degeneration in the elderly, which is very important for protecting vision. Here, we introduce the first metabolomic analysis of Sphingopyxis sp. USTB-05, aiming to shed light on the biosynthesis of carotenoids. Sphingopyxis sp. USTB-05 has the complete methylerythritol 4-phosphate (MEP) pathway and carotenoid biosynthesis pathway, especially involved in the bioconversion of zeaxanthin, violaxanthin, and astaxanthin. Metabolomic profiling identified seven carotenes and six xanthophylls synthesized by Sphingopyxis sp. USTB-05. Zeaxanthin, in particular, was found to be the most abundant, with a content of 37.1 µg/g dry cells. Collectively, the results presented herein greatly enhance our understanding of Sphingopyxis sp. USTB-05 in carotenoids biosynthesis, and thus further accelerate its fundamental molecular investigations and biotechnological applications.

Damage to the behavior and physiological functions of Apis mellifera (Hymenoptera: Apidae) by monocrotaline via the modulation of tryptophan metabolism and the corazonin receptor.

Monocrotaline (MCT) is a toxic pyrrolizidine alkaloid found in plants of the Crotalaria genus. As primary pollinators of Crotalaria plants, honeybees come into contact with this harmful substance. However, limited research has been conducted on the effects of MCT on Apis mellifera, particularly the risks of long-term exposure to sublethal concentrations. Through evaluating the proboscis extension reflex (PER) ability, analyzing the honeybee brain transcriptome, and analyzing the honeybee hemolymph metabolome, we discovered that sublethal concentrations of MCT impair the olfactory and memory capabilities of honeybees by affecting tryptophan (Trp) metabolism. Furthermore, MCT upregulates the expression of the corazonin receptor (CrzR) gene in the honeybee brain, which elevates reactive oxygen species (ROS) levels in the brain while reducing glucose levels in the hemolymph, consequently shortening the honeybees' lifespan. Our findings regarding the multifaceted impact of MCT on honeybees lay the foundation for exploring its toxicological pathways and management in honeybee populations.

Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin.

BACKGROUND: Sex differences exist in the prevalence and progression of major glomerular diseases. Podocytes are the essential cell-type in the kidney which maintain the physiological blood-urine barrier, and pathological changes in podocyte homeostasis are critical accelerators of impairment of kidney function. However, sex-specific molecular signatures of podocytes under physiological and stress conditions remain unknown. This work aimed at identifying sexual dimorphic molecular signatures of podocytes under physiological condition and pharmacologically challenged homeostasis with mechanistic target of rapamycin (mTOR) inhibition. mTOR is a crucial regulator involved in a variety of physiological and pathological stress responses in the kidney and inhibition of this pathway may therefore serve as a general stress challenger to get fundamental insights into sex differences in podocytes. METHODS: The genomic ROSAmT/mG-NPHS2 Cre mouse model was used which allows obtaining highly pure podocyte fractions for cell-specific molecular analyses, and vehicle or pharmacologic treatment with the mTOR inhibitor rapamycin was performed for 3 weeks. Subsequently, deep RNA sequencing and proteomics were performed of the isolated podocytes to identify intrinsic sex differences. Studies were supplemented with metabolomics from kidney cortex tissues. RESULTS: Although kidney function and morphology remained normal in all experimental groups, RNA sequencing, proteomics and metabolomics revealed strong intrinsic sex differences in the expression levels of mitochondrial, translation and structural transcripts, protein abundances and regulation of metabolic pathways. Interestingly, rapamycin abolished prominent sex-specific clustering of podocyte gene expression and induced major changes only in male transcriptome. Several sex-biased transcription factors could be identified as possible upstream regulators of these sexually dimorphic responses. Concordant to transcriptomics, metabolomic changes were more prominent in males. Remarkably, high number of previously reported kidney disease genes showed intrinsic sexual dimorphism and/or different response patterns towards mTOR inhibition. CONCLUSIONS: Our results highlight remarkable intrinsic sex-differences and sex-specific response patterns towards pharmacological challenged podocyte homeostasis which might fundamentally contribute to sex differences in kidney disease susceptibilities and progression. This work provides rationale and an in-depth database for novel targets to be tested in specific kidney disease models to advance with sex-specific treatment strategies.

The global burden of chronic kidney diseases is rapidly increasing and is projected to become the fifth most common cause of years of life lost worldwide by 2040. Sexual dimorphism in kidney diseases and transplantation is well known, yet sex-specific therapeutic strategies are still missing. One reason is the lack of knowledge due to the lack of inclusion of sex as a biological variable in study designs. This work aimed at identification of molecular signatures of male and female podocytes, gate-keepers of the glomerular filtration barrier. Like cardiomyocytes, podocytes are terminally differentiated cells which are highly susceptible towards pathological challenges. Podocytes are the decisive cell-type of the kidney to maintain the physiological blood-urine barrier, and disturbances of their homeostasis critically accelerate kidney function impairment. By help of a genomic mouse model, highly purified podocytes were obtained from male and female mice with and without pharmacological challenge of the mechanistic target of rapamycin (mTOR) signaling pathway which is known to be deregulated in major kidney diseases. Deep RNA sequencing, proteomics and metabolomics revealed strong intrinsic sex differences in the expression levels of mitochondrial, translation and structural transcripts, protein abundances and regulation of metabolic pathways which might fundamentally contribute to sex differences in kidney disease susceptibilities and progression. Remarkably, high number of previously reported kidney disease genes showed so far unknown intrinsic sexual dimorphism and/or different response patterns towards mTOR inhibition. Our work provides an in-depth database for novel targets to be tested in kidney disease models to advance with sex-specific treatment strategies.

Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and Eimeria tenella challenge.

Coccidiosis, caused by Eimeria parasites, significantly impacts poultry farm economics and animal welfare. Beyond its direct impact on health, Eimeria infection disrupts enteric microbial populations leading to dysbiosis and increases vulnerability to secondary diseases such as necrotic enteritis, caused by Clostridium perfringens. The impact of Eimeria infection or anticoccidial vaccination on host gastrointestinal phenotypes and enteric microbiota remains understudied. In this study, the metabolomic profiles and microbiota composition of chicken caecal tissue and contents were evaluated concurrently during a controlled experimental vaccination and challenge trial. Cobb500 broilers were vaccinated with a Saccharomyces cerevisiae-vectored anticoccidial vaccine and challenged with 15,000 Eimeria tenella oocysts. Assessment of caecal pathology and quantification of parasite load revealed correlations with alterations to caecal microbiota and caecal metabolome linked to infection and vaccination status. Infection heightened microbiota richness with increases in potentially pathogenic species, while vaccination elevated beneficial Bifidobacterium. Using a multi-omics factor analysis, data on caecal microbiota and metabolome were integrated and distinct profiles for healthy, infected, and recovering chickens were identified. Healthy and recovering chickens exhibited higher vitamin B metabolism linked to short-chain fatty acid-producing bacteria, whereas essential amino acid and cell membrane lipid metabolisms were prominent in infected and vaccinated chickens. Notably, vaccinated chickens showed distinct metabolites related to the enrichment of sphingolipids, important components of nerve cells and cell membranes. Our integrated multi-omics model revealed latent biomarkers indicative of vaccination and infection status, offering potential tools for diagnosing infection, monitoring vaccination efficacy, and guiding the development of novel treatments or controls.IMPORTANCEAdvances in anticoccidial vaccines have garnered significant attention in poultry health management. However, the intricacies of vaccine-induced alterations in the chicken gut microbiome and its subsequent impact on host metabolism remain inadequately explored. This study delves into the metabolic and microbiotic shifts in chickens post-vaccination, employing a multi-omics integration analysis. Our findings highlight a notable synergy between the microbiome composition and host-microbe interacted metabolic pathways in vaccinated chickens, differentiating them from infected or non-vaccinated cohorts. These insights pave the way for more targeted and efficient approaches in poultry disease control, enhancing both the efficacy of vaccines and the overall health of poultry populations.

Triple three-dimensional MS/MS spectrum facilitates quantitative ginsenosides-targeted sub-metabolome characterization in notoginseng.

Although serving as the workhorse, MS/MS cannot fully satisfy the analytical requirements of quantitative sub-metabolome characterization. Because more information intrinsically correlates to more structural and concentration clues, here, efforts were devoted to comprehensively tracing and deciphering MS/MS behaviors through constructing triple three-dimensional (3×3D)-MS/MS spectrum. Ginsenosides-targeted metabolomics of notoginseng, one of the most famous edible medicinal plants, was employed as a proof-of-concept. Serial authentic ginsenosides were deployed to build the correlations between 3×3D-MS/MS spectra and structure/concentration features. Through assaying ginsenosides with progressive concentrations using QTOF-MS to configure 1st 3D spectrum, the generations of MS1 spectral signals, particularly multi-charged multimer anions, e.g., [2M-2H]2- and [2M+2HCOO]2- ions, relied on both concentration and the amount of sugar chains. By programming progressive collision energies to the front collision cell of Qtrap-MS device to gain 2nd 3D spectrum, optimal collision energy (OCE) corresponding to the glycosidic bond fission was primarily correlated with the masses of precursor and fragment ions and partially governed by the glycosidation site. The quantitative relationships between OCEs and masses of precursor and fragment ions were utilized to build large-scale quantitative program for ginsenosides. After applying progressive exciting energies to the back collision chamber to build 3rd 3D spectrum, the fragment ion and the decomposition product anion exhibited identical dissociation trajectories when they shared the same molecular geometry. After ginsenosides-focused quantitative metabolomics, significant differences occurred for sub-metabolome amongst different parts of notoginseng. The differential ginsenosides were confirmatively identified by applying the correlations between 3×3D-MS/MS spectra and structures. Together, 3×3D-MS/MS spectrum covers all MS/MS behaviors and dramatically facilitates sub-metabolome characterization from both quantitative program development and structural identification.

Applicability of metabolomics to improve sustainable grapevine production.

Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system's response to genetic and environmental changes, providing a more accurate description of plants' phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.

Meat exudate metabolomics reveals the impact of freeze-thaw cycles on meat quality in pork loins.

The aim of this study was to explore the effects of freeze-thaw (FT) cycles on meat quality, myofibrillar protein gelation and emulsification properties, and exudate metabolome changes in pork loins. Meat tenderness improved (P < 0.05), whereas water-holding capacity (WHC), meat color attributes declined (P < 0.05) with FT cycles. Multiple FT accelerated meat lipid and protein oxidations. Decreases in strength and WHC of myofibrillar protein gels with FT cycles were confirmed. Myofibrillar protein emulsions with more FT cycles showed a decrease in the emulsifying activity index (P < 0.001) and larger oil droplets, resulting in poorer storage stability. A total of 501 metabolites were tentatively identified in pork exudates, with 21 metabolites significantly correlated (P < 0.05 and r > 0.6) with meat quality attributes. These results demonstrated the potential of using the metabolomic information from exudates to elaborate on or even predict the FT cycles, or meat quality.

Metabolomics and proteomics in pheochromocytoma and paraganglioma: Translating biochemistry and biology to bedside.

The complexity of omes - the key cellular ensembles (genome and epigenome, transcriptome, proteome, and metabolome) - is becoming increasingly understood in terms of big-data analysis, the omics. Amongst these, proteomics provides a global description of quantitative and qualitative alterations of protein expression (or protein abundance in body fluids) in response to physiologic or pathologic processes while metabolomics offers a functional portrait of the physiological state by quantifying metabolite abundances in biological samples. Here, we summarize how different techniques of proteomic and metabolic analysis can be used to define key biochemical characteristics of pheochromocytomas/paragangliomas (PPGL). The significance of omics in understanding features of PPGL biology that might translate to improved diagnosis and treatment will be highlighted.