Dynamic changes of rumen microbiota and serum metabolome revealed increases in meat quality and growth performances of sheep fed bio‑fermented rice straw

Background Providing high-quality roughage is crucial for improvement of ruminant production because it is an essential component of their feed.Our previous study showed that feeding bio-fermented rice straw(BF)improved the feed intake and weight gain of sheep.However,it remains unclear why feeding BF to sheep increased their feed intake and weight gain.Therefore,the purposes of this research were to investigate how the rumen micro-biota and serum metabolome are dynamically changing after feeding BF,as well as how their changes influence the feed intake,digestibility,nutrient transport,meat quality and growth performances of sheep.Twelve growing Hu sheep were allocated into 3 groups:alfalfa hay fed group(AH:positive control),rice straw fed group(RS:negative control)and BF fed group(BF:treatment).Samples of rumen content,blood,rumen epithelium,muscle,feed offered and refusals were collected for the subsequent analysis.Results Feeding BF changed the microbial community and rumen fermentation,particularly increasing(P<0.05)relative abundance of Prevotella and propionate production,and decreasing(P<0.05)enteric methane yield.The histomorphology(height,width,area and thickness)of rumen papillae and gene expression for carbohydrate trans-port(MCT1),tight junction(claudin-1,claudin-4),and cell proliferation(CDK4,Cyclin A2,Cyclin E1)were improved(P<0.05)in sheep fed BF.Additionally,serum metabolome was also dynamically changed,which led to up-regulating(P<0.05)the primary bile acid biosynthesis and biosynthesis of unsaturated fatty acid in sheep fed BF.As a result,the higher(P<0.05)feed intake,digestibility,growth rate,feed efficiency,meat quality and mono-unsaturated fatty acid concentration in muscle,and the lower(P<0.05)feed cost per kg of live weight were achieved by feeding BF.Conclusions Feeding BF improved the growth performances and meat quality of sheep and reduced their feed cost.Therefore,bio-fermentation of rice straw could be an innovative way for improving ruminant production with mini-mizing production costs.

Nostoc commune Vauch. polysaccharide alleviates Pb-induced hepatorenal toxicity by changing gut bacteriome, mycobiome, and metabolome

This study aimed to explore the protective effect and potential mechanism of Nostoc commune Vauch.polysaccharide(NCVP)on lead(Pb)-poisoning mice.NCVP improved Pb-induced hepatorenal toxicity and inflammatory responses and modulated key indicators of antioxidant capacity.Moreover,the down-regulation of critical proteins of the Nrf2 pathway induced by Pb could be reversed after NCVP intervention.In addition,NCVP maintained the diversity of gut bacteriobiota and restored the relative abundance of f_Prevotellaceae,g_Alloprevotella,and f_Eubacterium_coprostanoligenes_group reduced by Pb.Also,NCVP regulated the diversity and abundance of gut mycobiota affected by Pb.Specifically,Pb decreased the proportion of pathogenic species(g_Fusarium,p_Basidiomycota,g_Alternaria,g_Aspergillus,and g_Candida)while NCVP increased the abundance of probiotics species(g_Kazachstania and p_Ascomycota).Furthermore,the metabolomic analysis found that NCVP significantly altered a range of microbial metabolites,including porphobilinogen,cromakalim,salidroside,and trichostatin A,which has significant associations with specific gut bacteriobiota or mycobiota.These altered metabolites are involved in primary bile acid biosynthesis,metabolism of xenobiotics by cytochrome P450,lysine degradation,and other metabolic pathways.Overall,our findings indicate that NCVP might be an excellent natural product for eliminating Pb-induced hepatorenal toxicity,possibly by regulating gut bacteriome,mycobiome and metabolome.

Supplementation of Lycium barbarum residue increases the growth rate of Tan sheep by enhancing their feed intake and regulating their rumen microbiome and metabolome

Lycium barbarum residue(LBR),a by-product of L.barbarum processing,is packed with bioactive components and can be potentially utilized as a feed additive in animal husbandry.However,the fundamental understanding of its effectiveness on livestock animals is still lacking,particularly in ruminants.To explore the effects of LBR on the growth performance,rumen fermentation parameters,ruminal microbes and metabolites of Tan sheep,sixteen fattening rams(aged 4 mon)were fed a basal diet(CON,n=8)or a basal diet supplemented with 5%LBR(LBR,n=8).The experiment lasted for 70 d,with 10 d adaptation period and 60 d treatment period.The results showed that the LBR enhanced the average daily feed intake,average daily gain(P<0.05),and ruminal total volatile fatty acids(P<0.01)while decreasing ammonia-nitrogen concentration and rumen pH value(P<0.05).Additionally,the LBR improved the relative abundances of Prevotella,Succiniclasticum,Ruminococcus,Coprococcus,Selenomonas,and Butyrivibrio(P<0.05)and reduced the relative abundances of Oscillospira and Succinivibrio(P<0.05).The LBR altered the ruminal metabolome(P<0.01)by increasing the abundances of ruminal metabolites involved in amino acids(e.g.,L-proline,L-phenylalanine,L-lysine,and L-tyrosine),pyrimidine metabolism(e.g.,uridine,uracil,and thymidine),and microbial protein synthesis(e.g.,xanthine and hypoxanthine).In conclusion,LBR had positive effects on the growth rate of Tan sheep as well as on rumen fermentation parameters,rumen microbiome and rumen metabolome.

Dynamic gut microbiome-metabolome in cationic bovine serum albumin induced experimental immune-complex glomerulonephritis and effect of losartan and mycophenolate mofetil on microbiota modulation

Dynamic changes in gut dysbiosis and metabolomic dysregulation are associated with immune-complex glomerulonephritis(ICGN).However,an in-depth study on this topic is currently lacking.Herein,we report an ICGN model to address this gap.ICGN was induced via the intravenous injection of cationized bovine serum albumin(c-BSA)into Sprague-Dawley(SD)rats for two weeks,after which mycophenolate mofetil(MMF)and losartan were administered orally.Two and six weeks after ICGN establishment,fecal samples were collected and 16S ribosomal DNA(rDNA)sequencing and untargeted metabolomic were conducted.Fecal microbiota transplantation(FMT)was conducted to determine whether gut normali-zation caused by MMF and losartan contributed to their renal protective effects.A gradual decline in microbial diversity and richness was accompanied by a loss of renal function.Approximately 18 genera were found to have significantly different relative abundances between the early and later stages,and Marvinbryantia and Allobaculum were markedly upregulated in both stages.Untargeted metabolomics indicated that the tryptophan metabolism was enhanced in ICGN,characterized by the overproduction of indole and kynurenic acid,while the serotonin pathway was reduced.Administration of losartan and MMF ameliorated microbial dysbiosis and reduced the accumulation of indoxyl conjugates in feces.FMT using feces from animals administered MMF and losartan improved gut dysbiosis by decreasing the Firmicutes/Bacteroidetes(F/B)ratio but did not improve renal function.These findings indicate that ICGN induces serous gut dysbiosis,wherein an altered tryptophan metabolism may contribute to its pro-gression.MMF and losartan significantly reversed the gut microbial and metabolomic dysbiosis,which partially contributed to their renoprotective effects.

Potential Secretory Transporters and Biosynthetic Precursors of Biological Nitrification Inhibitor 1,9-Decanediol in Rice as Revealed by Transcriptome and Metabolome Analyses

Biological nitrification inhibitors(BNIs)are released from plant roots and inhibit the nitrification activity of microorganisms in soils,reducing NO_(3)^(‒)leaching and N2O emissions,and increasing nitrogenuse efficiency(NUE).Several recent studies have focused on the identification of new BNIs,yet little is known about the genetic loci that govern their biosynthesis and secretion.We applied a combined transcriptomic and metabolomic analysis to investigate possible biosynthetic pathways and transporters involved in the biosynthesis and release of BNI 1,9-decanediol(1,9-D),which was previously identified in rice root exudates.Our results linked four fatty acids,icosapentaenoic acid,linoleate,norlinolenic acid,and polyhydroxy-α,ω-divarboxylic acid,with 1,9-D biosynthesis and three transporter families,namely the ATP-binding cassette protein family,the multidrug and toxic compound extrusion family,and the major facilitator superfamily,with 1,9-D release from roots into the soil medium.Our finding provided candidates for further work on the genes implicated in the biosynthesis and secretion of 1,9-D and pinpoint genetic loci for crop breeding to improve NUE by enhancing 1,9-D secretion,with the potential to reduce NO_(3)^(‒)leaching and N2O emissions from agricultural soils.

Effect of biochar on the metabolome of soybean seedlings

The use of biochar can have several effects on plant germination,depending on raw material,preparation method and application dose.However,the molecular mechanisms that lead to those results have yet to be elucidated.The aim of this research was to improve the understanding of these mechanisms by characterizing the metabolic effects of sugarcane bagasse biochar on soybean germination.Three types of biochars were prepared by pyrolysis at 300℃(SCB300),400℃(SCB400)and 600℃(SCB600).Then,each one was mixed into sand at 1%,3%,5%(w/w)dose,respectively.The experiment was performed in 8 days of incubation,when the number of germinated seeds and the average radicle length were determined.To evaluate the metabolome,the dry biomass(DB)was subjected to extraction with a mixture of methanol-d4 and D2O(1:1 v/v).The extracts were submitted to metabolomics analysis by Proton Nuclear Magnetic Resonance.The Relative Germination,Relative Average Radicle Growth and Germination Index increased in all treatments compared to control.On the other hand,the DB increased in all treatments,except for SCB300,at doses of 1%and 3%w/w.Seven metabolites(alanine,asparagine,acetic acid,citric acid,glycerol,fatty acids and sucrose)were identified and quantified in DB extracts as the most influential finding for the separation of treatments.Taken together,these results strongly suggested that biochars accelerated the catabolism of triacylglycerols to sucrose and induced a slight osmotic stress.

Comparison of transcriptome and metabolome analysis revealed differences in cold resistant metabolic pathways in different apple cultivars under low temperature stress

Freezing injury in winter is an important abiotic stress that seriously affects plant growth and development.Deciduous fruit trees resist freezing injury by inducing dormancy.However,different cultivars of the same species have different cold resistance strategies.Little is known about the molecular mechanism of apple trees in response to freezing injury during winter dormancy.Therefore,in this study,1-year-old branches of the cold-resistant cultivar‘Hanfu’(HF)and the cold-sensitive cultivar‘Changfuji No.2’(CF)were used to explore their cold resistance through physiological,biochemical,transcriptomics,and metabolomics analyses.Combining physiological and biochemical data,we found that HF had a stronger osmotic regulation ability and antioxidant enzyme activity than CF,as well as stronger cold resistance.The functional enrichment analysis showed that both cultivars were significantly enriched in pathways related to signal transduction,hormone regulation,and sugar metabolism under freezing stress.In addition,the differentially expressed genes(DEGs)encoding galactinol synthase,raffinose synthase,and stachyose synthetase in raffinose family oligosaccharides(RFOs)metabolic pathways were upregulated in HF,and raffinose and stachyose were accumulated,while their contents in CF were lower.HF accumulated 4-aminobutyric acid,spermidine,and ascorbic acid to scavenge reactive oxygen species(ROS).While the contents of oxidized glutathione,vitamin C,glutathione,and spermidine in CF decreased under freezing stress,consequently,the ability to scavenge ROS was low.Furthermore,the transcription factors apetala 2/ethylene responsive factor(AP2/ERF)and WRKY were strongly induced under freezing stress.In summary,the difference in key metabolic components of HF and CF under freezing stress is the major factor affecting their difference in cold resistance.The obtained results deepen our understanding of the cold resistance mechanism in apple trees in response to freezing injury during dormancy.

Dietary bamboo leaf flavonoids improve quality and microstructure of broiler meat by changing untargeted metabolome

Background Dietary bamboo leaf flavonoids(BLFs)are rarely used in poultry production,and it is unknown whether they influence meat texture profile,perceived color,or microstructure.Results A total of 720 one-day-old Arbor Acres broilers were supplemented with a basal diet with 20 mg bacitracin/kg,50 mg BLFs/kg,or 250 mg BLFs/kg or without additions.Data showed that the dietary BLFs significantly(P<0.05)changed growth performance and the texture profile.In particular,BLFs increased birds’average daily gain and average daily feed intake,decreased the feed:gain ratio and mortality rate,improved elasticity of breast meat,enhanced the gumminess of breast and leg meat,and decreased the hardness of breast meat.Moreover,a significant(P<0.05)increase in redness(a*)and chroma(c*)of breast meat and c*and water-holding capacity of leg meat was found in BLF-supplemented broilers compared with control broilers.In addition,BLFs supplementation significantly decreased(P<0.05)theβ-sheet ratio and serum malondialdehyde and increased theβ-turn ratio of protein secondary structure,superoxide dismutase,and glutathione peroxidase of breast meat and total antioxidant capacity and catalase of serum.Based on the analysis of untargeted metabolome,BLFs treatment considerably altered 14 metabolites of the breast meat,including flavonoids,amino acids,and organic acids,as well as phenolic and aromatic compounds.Conclusions Dietary BLFs supplementation could play a beneficial role in improving meat quality and sensory color in the poultry industry by changing protein secondary structures and modulating metabolites.

Mechanism of Learning and Memory Impairment in Rats Exposed to Arsenic and/or Fluoride Based on Microbiome and Metabolome

Objective Arsenic(As) and fluoride(F) are two of the most common elements contaminating groundwater resources. A growing number of studies have found that As and F can cause neurotoxicity in infants and children, leading to cognitive, learning, and memory impairments. However, early biomarkers of learning and memory impairment induced by As and/or F remain unclear. In the present study, the mechanisms by which As and/or F cause learning memory impairment are explored at the multi-omics level(microbiome and metabolome).Methods We stablished an SD rats model exposed to arsenic and/or fluoride from intrauterine to adult period.Results Arsenic and/fluoride exposed groups showed reduced neurobehavioral performance and lesions in the hippocampal CA1 region. 16S rRNA gene sequencing revealed that As and/or F exposure significantly altered the composition and diversity of the gut microbiome, featuring the Lachnospiraceae_NK4A136_group, Ruminococcus_1, Prevotellaceae_NK3B31_group, [Eubacterium]_xylanophilum_group. Metabolome analysis showed that As and/or F-induced learning and memory impairment may be related to tryptophan, lipoic acid, glutamate, gamma-aminobutyric acidergic(GABAergic) synapse, and arachidonic acid(AA) metabolism. The gut microbiota, metabolites, and learning memory indicators were significantly correlated.Conclusion Learning memory impairment triggered by As and/or F exposure may be mediated by different gut microbes and their associated metabolites.

Integrative analysis of the transcriptome and metabolome reveals the response mechanism to tomato spotted wilt virus

Tomato spotted wilt virus(TSWV)is an important virus that has rapidly spread throughout the world.TSWV seriously hinders the production of tomato(Solanum lycopersicum)and other plants.In order to discover more new genes and metabolites related to TSWV resistance in tomato plants,the genes and metabolites related to the resistance of tomato plants inoculated with TSWV were identified and studied herein.The tomato TSWV-resistance line YNAU335(335)and TSWV-susceptible lines NO5 and 96172I(961)were used as the transcriptome and metabolome research materials.Transcriptomic and metabolomic techniques were used to analyze the gene and metabolite response mechanisms to TSWV inoculation.A total of 3566,2951,and 2674 differentially expressed genes(DEGs)were identified in lines 335,NO5,and961,respectively.Meanwhile,208,228,and 273 differentially accumulated metabolites(DAMs)were identified in lines 335,NO5,and 961,respectively.In line 335,the number of DEGs was the highest,but the number of DAMs was lowest.Furthermore,903 DEGs and 94 DAMs were common to the response to TSWV in the three inbred lines.The 903 DEGs and 94 DAMs were mainly enriched in the plant hormone signal transduction and flavonoid synthesis pathways.In addition,many nucleotide-binding site-leucine-rich repeat genes and transcription factors were found that might be involved in the TSWV response.These results provide new insights into TSWV resistance mechanisms.

Changes of the liver metabolome following an intravenous lipopolysaccharide injection in Holstein cows supplemented with dietary carnitine

Background:Carnitine facilitates the flux of long-chain fatty acids for hepatic mitochondrial beta-oxidation,which acts to ameliorate the negative energy balance commonly affecting high-yielding dairy cows.Inflammation triggered by lipopolysaccharide(LPS)load can however pose a challenge to the metabolic integrity via the expression of pro-inflammatory mediators,leading to immune system activation and respective metabolic alterations.The effect of enhanced carnitine availability on hepatic metabolome profiles during an inflammatory challenge has not yet been determined in dairy cows.Herein,Holstein cows were supplemented with 25 g/d rumen-protected carnitine from 42d prepartum until 126 d postpartum(n=16)or assigned to the control group with no supplementation during the same period(n=14).We biopsied the liver of the cows before(100 d postpartum)and after(112 d postpartum)an intravenous injection of 0.5μg/kg LPS.Liver samples were subjected to a targeted metabolomics analysis using the AbsoluteIDQ p180 Kit(Biocrates Life Sciences AG,Innsbruck,Austria).Results:Multivariate statistical analyses revealed that hepatic metabolome profiles changed in relation to both the carnitine supplementation and the LPS challenge.Comparing the metabolite profiles on 100 d,carnitine increased the concentration of short-and long-chain acyl-carnitines,which may be explained by an enhanced mitochondrial fatty acid shuttle and hence greater energy availability.The LPS injection affected hepatic metabolite profiles only in the carnitine supplemented group,particularly altering the concentration of biogenic amines.Conclusions:Our results point to interactions between an acute hepatic inflammatory response and biogenic amine metabolism,depending on energy availability.

Transcriptome and Metabolome Revealed the Mechanism of NtBRL3 Overexpression Tobacco(Nicotiana tabacum L.K326)in Response to Drought Stress

Drought has severely affected the yield and quality of commercial crops.The BRI1 family plays an important role in plant response to drought stress,and BRL3 gene plays an important role in the study of drought in Arabidopsis thaliana.In this study,NtBRL3 was constructed as a vector and genetically transformed to obtain‘N.Tobacco K326’overexpression of NtBRL3.The enzyme activities of transgenic tobacco and wild-type tobacco were measured and transcriptome and metabolome analyses were performed.The results showed that the antioxidant enzymes of transgenic tobacco were more active under drought conditions,and 85 significantly differentially metabolites and 106 significantly differentially expressed genes were identified in the metabolome and transcriptome analyses,respectively.Transgenic tobacco NtBRL3ox demonstrated an excessive accumulation of droughtrelated metabolites,sugars such as sucrose and maltotetraose,and amino acids such as proline,compared with WT.We discovered drought-related differential genes in the root transcriptome,among which LOX6,RD22,WSD1,CCD8,and UGT were key genes which play an important role in plant response to drought stress.Our results demonstrate that NtBRL3 overexpression in K326 enhances drought resistance in transgenic tobacco.

Analysis of Differential Metabolites in Selenium-enriched Rice Based on Extensive Non-targeted Metabolome

[Objectives]Selenium(Se)-enriched rice is the main type of Se-enriched agricultural product developed in China,and this study aimed to understand the impact of selenium application on the metabolites in rice.[Methods]Se-enriched rice was prepared by foliar application of a sodium selenite aqueous solution,and high-throughput analysis of differential metabolites in Se-enriched rice was conducted based on extensive non-targeted metabolome.[Results]There were significant differences in metabolites between Se-enriched rice and ordinary rice,and a total of 535 differential metabolites were identified.Among them,420 metabolites in Se-enriched rice were upregulated,accounting for 78.5%,far higher than downregulated metabolites.The enrichment differences of three KEGG metabolic pathways,including cysteine and methionine metabolism,zeatin biosynthesis,and arachidonic acid metabolism,reached a significant level,indicating that selenium enrichment had a significant regulatory effect on the metabolism of sulfur-containing amino acids,the synthesis of natural cytokinin zeatin,and arachidonic acid bioactive components in rice.[Conclusions]The results can provide a theoretical basis for the production of Se-enriched rice.

Dynamic alterations in the gut microbiota and metabolome during the development of methionine-choline-deficient diet-induced nonalcoholic steatohepatitis

AIM To investigate changes in gut microbiota and metabolism during nonalcoholic steatohepatitis(NASH) development in mice fed a methionine-choline-deficient(MCD) diet. METHODS Twenty-four male C57 BL/6 J mice were equally divided into four groups and fed a methionine-choline-sufficient diet for 2 wk(Control 2 w group,n = 6) or 4 wk(Control 4 w group,n = 6) or the MCD diet for 2 wk(MCD 2 w group,n = 6) or 4 wk(MCD 4 w group,n = 6). Liver injury,fibrosis,and intestinal barrier function were evaluated after 2 and 4 wk of feeding. The fecal microbiome and metabolome were studied using 16 s r RNA deep sequencing and gas chromatography-mass spectrometry. RESULTS The mice fed the MCD diet presented with simple hepatic steatosis and slight intestinal barrier deterioration after 2 wk. After 4 wk of feeding with the MCD diet,however,the mice developed prominent NASH with liver fibrosis,and the intestinal barrier was more impaired. Compared with the control diet,the MCD diet induced gradual gut microbiota dysbiosis,as evidenced by a marked decrease in the abundance of Alistipes and the(Eubacterium) coprostanoligenes group(P < 0.001 and P < 0.05,respectively) and a significant increase in Ruminococcaceae UCG 014 abundance(P < 0.05) after 2 wk. At 4 wk,the MCD diet significantly reduced the promising probiotic Bifidobacterium levels and markedly promoted Bacteroides abundance(P < 0.05,and P < 0.01,respectively). The fecal metabolomic profile was also substantially altered by the MCD diet: At 2 wk,arachidic acid,hexadecane,palmitic acid,and tetracosane were selected as potential biomarkers that were significantly different in the corresponding control group,and at 4 wk,cholic acid,cholesterol,arachidic acid,tetracosane,and stearic acid were selected. CONCLUSION The MCD diet induced persistent alterations in the gut microbiota and metabolome.

Alterations of the gut microbiome and metabolome in alcoholic liver disease

Alcohol consumption is one of the leading causes of liver diseases and liver-related death worldwide. The gut is a habitat for billions of microorganisms which promotes metabolism and digestion in their symbiotic relationship with the host. Alterations of gut microbiome by alcohol consumption are referred to bacterial overgrowth, release of bacteria-derived products, and/or changed microbiota equilibrium. Alcohol consumption also perturbs the function of gastrointestinal mucosa and elicits a pathophysiological condition. These adverse effects caused by alcohol may ultimately result in a broad change of gastrointestinal luminal metabolites such as bile acids, short chain fatty acids, and branched chain amino acids. Gut microbiota alterations, metabolic changes produced in a dysbiotic intestinal environment, and the host factors are all critical contributors to the development and progression of alcoholic liver disease. This review summarizes recent findings of how alcohol-induced alterations of gut microbiota and metabolome, and discusses the mecha-nistic link between gastrointestinal dyshomeostasis and alcoholic liver injury.

Response of gut microbiota to serum metabolome changes in intrahepatic cholestasis of pregnant patients

BACKGROUND Intrahepatic cholestasis in pregnancy(ICP)is the most common liver disease during pregnancy,and its exact etiology and course of progression are still poorly understood.AIM To investigate the link between the gut microbiota and serum metabolome in ICP patients.METHODS In this study,a total of 30 patients were recruited,including 15 patients with ICP(disease group)and 15 healthy pregnant patients(healthy group).The serum nontarget metabolomes from both groups were determined.Amplification of the 16S rRNA V3-V4 region was performed using fecal samples from the disease and healthy groups.By comparing the differences in the microbiota and metabolite compositions between the two groups,the relationship between the gut microbiota and serum metabolites was also investigated.RESULTS The Kyoto Encyclopedia of Genes and Genomes analysis results showed that the primary bile acid biosynthesis,bile secretion and taurine and hypotaurine metabolism pathways were enriched in the ICP patients compared with the healthy controls.In addition,some pathways related to protein metabolism were also enriched in the ICP patients.The principal coordination analysis results showed that there was a distinct difference in the gut microbiota composition(beta diversity)between the ICP patients and healthy controls.At the phylum level,we observed that the relative abundance of Firmicutes was higher in the healthy group,while Bacteroidetes were enriched in the disease group.At the genus level,most of the bacteria depleted in ICP are able to produce short-chain fatty acids(e.g.,Faecalibacterium,Blautia and Eubacterium hallii),while the bacteria enriched in ICP are associated with bile acid metabolism(e.g.,Parabacteroides and Bilophila).Our results also showed that specific genera were associated with the serum metabolome.CONCLUSION Our study showed that the serum metabolome was altered in ICP patients compared to healthy controls,with significant differences in the bile,taurine and hypotaurine metabolite pathways.Alterations in the metabolization of these pathways may lead to disturbances in the gut microbiota,which may further affect the course of progression of ICP.

Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L.

We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate(Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis(WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage(stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage(stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.

The metabolome identity:basis for discovery of biomarkers in neurodegeneration

Neurodegenerative disorders are often associated with cellular dysfunction caused by underlying protein-misfolding signalling. Numerous neuropathologies are diagnosed at late stage symptomatic changes which occur in response to these molecular malfunctions and treatment is often too late or restricted only to the slowing of further cell death. Important new strategies to identify early biomarkers with predictive value to intervene with disease progression at stages where cell dysfunction has not progressed irreversibly is of paramount importance. Thus, the identification of these markers presents an essential opportunity to identify and target disease pathways. This review highlights some important metabolic alterations detected in neurodegeneration caused by misfolded prion protein and discusses common toxicity pathways identified across different neurodegenerative diseases. Thus, having established some commonalities between various degenerative conditions, detectable metabolic changes may be of extreme value as an early diagnostic biomarker in disease.

Protective effect of natural products and hormones in colon cancer using metabolome:A physiological overview

Globally, the third cause of males cancer and the fourth cause of females cancer is colon cancer(CC). In Egypt, high CC percentage occurs in children and in individuals below 40 years of age. The complete loss of biological enzyme function is the main cause of CC and consequently CC increased in smoking and pollution exposure. The aim of this review is to focus on the application of metabolome as a physiological tool that can play an important role in preventing CC incidence by natural products and hormones. The dietary factors, intestinal micro-flora and endogenously produced metabolites are the main three causes that produce free radicals in the colon. A correlation occurs between the enzyme activity and CC polymorphisms or property. Nowadays metabolome is applied with the progress of different analytical methods, data bases and tools for cancer predication and stimulation especially in CC cases. Metabolism is defined as intracellular chemical reactions that produce chemical substances and energies sustaining life. Metabolic pathway networks are also composed of links that are defined as transformation of chemical structures between two metabolites and an enzyme reaction. The most important advantage of metabolome is its ability to analyze metabolites from any source, regardless of origin, where the application of liquid chromatography combined with mass spectra in metabolome analysis to a series of cancer cell lines that were progressively more tumorigenic due to the induction of 1,2,3 or 4 oncogenes to cell lines could be a metabolome example application. In conclusion, natural products and hormones are very important in preventing CC in humans and animal models where both natural products and hormones play a significant and important effect in regulating physiological process especially in CC cases. In this situation, metabolome must increase in its application in the future for the diagnosis of CC cases.

Characterization of gut microbiome and metabolome in Helicobacter pylori patients in an underprivileged community in the United States

BACKGROUND Helicobacter pylori(H.pylori),a bacterium that infects approximately half of the world’s population,is associated with various gastrointestinal diseases,including peptic ulcers,non-ulcer dyspepsia,gastric adenocarcinoma,and gastric lymphoma.As the burden of antibiotic resistance increases,the need for new adjunct therapies designed to facilitate H.pylori eradication and reduce negative distal outcomes associated with infection has become more pressing.Characterization of the interactions between H.pylori,the fecal microbiome,and fecal fatty acid metabolism,as well as the mechanisms underlying these interactions,may offer new therapeutic approaches.AIM To characterize the gut microbiome and metabolome in H.pylori patients in a socioeconomically challenged and underprivileged inner-city community.METHODS Stool samples from 19 H.pylori patients and 16 control subjects were analyzed.16S rRNA gene sequencing was performed on normalized pooled amplicons using the Illumina MiSeq System using a MiSeq reagent kit v2.Alpha and beta diversity analyses were performed in QIIME 2.Non-targeted fatty acid analysis of the samples was carried out using gas chromatography-mass spectrometry,which measures the total content of 30 fatty acids in stool after conversion into their corresponding fatty acid methyl esters.Multi-dimensional scaling(MDS)was performed on Bray-Curtis distance matrices created from both the metabolomics and microbiome datasets and a Procrustes test was performed on the metabolomics and microbiome MDS coordinates.RESULTS Fecal microbiome analysis showed that alpha diversity was lowest in H.pylori patients over 40 years of age compared to control subjects of similar age group.Beta diversity analysis of the samples revealed significant differences in microbial community structure between H.pylori patients and control subjects across all ages.Thirty-eight and six taxa had lower and higher relative abundance in H.pylori patients,respectively.Taxa that were enriched in H.pylori patients included Atopobium,Gemellaceae,Micrococcaceae,Gemellales and Rothia(R.mucilaginosa).Notably,relative abundance of the phylum Verrucomicrobia was decreased in H.pylori patients compared to control subjects.Procrustes analysis showed a significant relationship between the microbiome and metabolome datasets.Stool samples from H.pylori patients showed increases in several fatty acids including the polyunsaturated fatty acids(PUFAs)22:4n6,22:5n3,20:3n6 and 22:2n6,while decreases were noted in other fatty acids including the PUFA 18:3n6.The pattern of changes in fatty acid concentration correlated to the Bacteroidetes:Firmicutes ratio determined by 16S rRNA gene analysis.CONCLUSION This exploratory study demonstrates H.pylori-associated changes to the fecal microbiome and fecal fatty acid metabolism.Such changes may have implications for improving eradication rates and minimizing associated negative distal outcomes.