PubMed

Front Microbiol. 2022 Dec 16;13:1032622. doi: 10.3389/fmicb.2022.1032622. eCollection 2022.ABSTRACTSupplementation of the sheep diet with oats (Avena sativa L.) improves animal growth and meat quality, however effects on intestinal microbes and their metabolites was not clear. This study aimed to establish the effect of dietary oat supplementation on rumen and colonic microbial abundance and explore the relationship with subsequent changes in digesta metabolites. Twenty Small-tail Han sheep were randomly assigned to a diet containing 30 g/100 g of maize straw (Control) or oat hay (Oat). After 90-days on experimental diets, rumen and colon digesta were collected and microbial diversity was determined by 16S rRNA gene Illumina NovaSeq sequencing and metabolomics was conducted using Ultra-high performance liquid chromatography Q-Exactive mass spectrometry (UHPLC-QE-MS). Compared to Control group, oat hay increased the abundance of Bacteroidetes and Fibrobacteres as well as known short-chain fatty acid (SCFA) producers Prevotellaceae, Ruminococcaceae and Fibrobacteraceae in rumen (p < 0.05). In rumen digesta, the Oat group showed had higher levels of (3Z,6Z)-3,6-nonadienal, Limonene-1,2-epoxide, P-tolualdehyde, and Salicylaldehyde compared to Control (p < 0.05) and these metabolites were positively correlated with the abundance of cecal Prevotellaceae NK3B31. In conclusion, supplementation of the sheep diet with oat hay improved desirable microbes and metabolites in the rumen, providing insight into mechanisms whereby meat quality can be improved by oat hay supplementation.PMID:36590432 | PMC:PMC9801518 | DOI:10.3389/fmicb.2022.1032622

Front Microbiol. 2022 Dec 14;13:1079136. doi: 10.3389/fmicb.2022.1079136. eCollection 2022.ABSTRACTThe use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.PMID:36590430 | PMC:PMC9801413 | DOI:10.3389/fmicb.2022.1079136

Front Microbiol. 2022 Dec 16;13:1039217. doi: 10.3389/fmicb.2022.1039217. eCollection 2022.ABSTRACTThis study was conducted to evaluate the effects of two glucogenic diets (C: ground corn and corn silage; S: steam-flaked corn and corn silage) and a lipogenic diet (L: sugar beet pulp and alfalfa silage) on the ruminal bacterial and archaeal structures, the metabolomic products, and gas production after 48 h in vitro fermentation with rumen fluid of dairy cows. Compared to the C and S diets, the L dietary treatment leaded to a lower dry matter digestibility (DMD), lower propionate production and ammonia-nitrogen concentration. The two glucogenic diets performed worse in controlling methane and lactic acid production compared to the L diet. The S diet produced the greatest cumulative gas volume at any time points during incubation compared to the C and L diet. The metabolomics analysis revealed that the lipid digestion especially the fatty acid metabolism was improved, but the amino acid digestion was weakened in the L treatment than in other treatments. Differences in rumen fermentation characteristics were associated with (or resulting from) changes in the relative abundance of bacterial and archaeal genera. The rumen fluid fermented with L diet had a significantly higher number of cellulolytic bacteria, including the genera of Ruminococcus, Butyrivibrio, Eubacterium, Lachnospira, unclassified Lachnospiraceae, and unclassified Ruminococcaceae. The relative abundances of amylolytic bacteria genera including Selenomonas_1, Ruminobacter, and Succinivibrionaceae_UCG-002 were higher in samples for diets C and S. The results indicated that the two glucogenic diets leaded to a higher relative abundance of bacteria which functions in succinate pathway resulting in a higher propionate production. The steam-flaked corn diet had a higher gas production and lower level of metabolites in fatty acids and amino acids. Most highly abundant bacteria were observed to be not sensitive to dietary alterations of starch and fiber, except for several amylolytic bacteria and cellulolytic bacteria. These finding offered new insights on the digesting preference of ruminal bacteria, which can assist to improve the rumen functioning.PMID:36590412 | PMC:PMC9800790 | DOI:10.3389/fmicb.2022.1039217

Front Nutr. 2022 Dec 14;9:1067597. doi: 10.3389/fnut.2022.1067597. eCollection 2022.ABSTRACTSprouts are recognized as nutritional and functional vegetables. In this study, 17 selected seeds were germinated simultaneously. The antioxidant capacity and total phenolic content (TPC) were determined for seeds and sprouts of all species. Both seed and sprout of white radish, with the highest antioxidant capacity, and TPC among all the 17 species, were further determined for phenolic metabolomics. Four phenolic classes with 316 phenolic metabolites were identified. 198 significantly different metabolites with 146 up-regulated and 52 down-regulated were confirmed, and high amounts of phenolic acids and flavonoids were found to be accumulated in the sprout. Several metabolism and biosynthesis, including phenylpropanoid, favone and flavonol, phenylalanine, and various secondary metabolites, were significantly activated. Significant correlations were found among FRAP, DPPH, ABTS, TPC, and phenolic profiles. Therefore, white radish sprout could be served as antioxidant and could be a good source of dietary polyphenols.PMID:36590202 | PMC:PMC9798843 | DOI:10.3389/fnut.2022.1067597

Front Endocrinol (Lausanne). 2022 Dec 16;13:1034818. doi: 10.3389/fendo.2022.1034818. eCollection 2022.ABSTRACTBACKGROUND: Diabetic kidney disease (DKD), as a serious microvascular complication of diabetes, has limted treatment options. It is reported that the Sacubitril/Valsartan (Sac/Val) can improve kidney function, and the disordered gut microbiota and part of its metabolites are related to the development of DKD. Therefore, we aim to explore whether the effect of Sac/Val on DKD is associated with the gut microbiota and related plasma metabolic profiles.METHODS: Male C57BL/6J mice were randomly divided into 3 groups: Con group (n = 5), DKD group (n = 6), and Sac/Val group (n = 6) . Sac/Val group was treated with Sac/Val solution. The intervention was given once every 2 days for 6 weeks. We measured the blood glucose and urine protein level of mice at different times. We then collected samples at the end of experiment for the 16s rRNA gene sequencing analysis and the untargeted plasma metabonomic analysis.RESULTS: We found that the plasma creatinine concentration of DKD-group mice was significantly higher than that of Con-group mice, whereas it was reduced after the Sac/Val treatment. Compared with DKD mice, Sac/Val treatment could decrease the expression of indicators related to EndMT and renal fibrosis like vimentin, collagen IV and fibronectin in kidney. According to the criteria of LDA ≥ 2.5 and p<0.05, LefSe analysis of gut microbiota identified 13 biomarkers in Con group, and 33 biomarkers in DKD group, mainly including Prevotella, Escherichia_Shigella and Christensenellaceae_R_7_group, etc. For the Sac/Val group, there were 21 biomarkers, such as Bacteroides, Rikenellaceae_RC9_gut_group, Parabacteroides, Lactobacillus, etc. Plasma metabolomics analysis identified a total of 648 metabolites, and 167 important differential metabolites were screened among groups. KEGG pathway of tryptophan metabolism: M and bile secretion: OS had the highest significance of enrichment.CONCLUSIONS: Sac/Val improves the renal function of DKD mice by inhibiting renal fibrosis. This drug can also regulate gut microbiota in DKD mice.PMID:36589853 | PMC:PMC9802116 | DOI:10.3389/fendo.2022.1034818

Front Endocrinol (Lausanne). 2022 Dec 16;13:1036559. doi: 10.3389/fendo.2022.1036559. eCollection 2022.ABSTRACTINTRODUCTION: Refractory peptic ulcers lead to perforation and hemorrhage, which are fatal. However, these remain a therapeutic challenge. Gastric mucosal blood flow is crucial in maintaining gastric mucosal health. It's reported that Glucagon-like peptide-2 (GLP-2), a gastrointestinal hormone, stimulated intestinal blood flow. However, the direct role of GLP-2 in gastric mucosal blood flow and metabolites remain unclear. Here, we speculated that GLP-2 might protect the gastric mucosa by increasing gastric mucosal blood flow and regulating metabolites. This study was conducted to evaluate the role of GLP-2 in gastric mucosal lesions and its underlying mechanism.METHODS: We analyzed endogenous GLP-2 during gastric mucosal injury in the serum. Rats were randomly divided into two groups, with 36 rats in each group as follows: (1) normal control group (NC1); (2) ethanol model group (EC1); rats in EC1 and NC1 groups were intragastrically administered ethanol (1 ml/200 g body weight) and distilled water (1 ml/200 g body weight). The serum was collected 10 min before intragastric administration and 15, 30, 60, 90, and 120 min after intragastric administration. Furthermore, additional male Sprague-Dawley rats were randomly divided into three groups, with six rats in each group as follows: (1) normal control group (NC); (2) ethanol model group (EC); (3) 10 μg/200 g body weight GLP-2 group (GLP-2). Rats in the NC and EC groups were intraperitoneally injected with saline. Those in the GLP-2 group were intraperitoneally injected with GLP-2. Thirty minutes later, rats in the EC and GLP-2 groups were intragastrically administered ethanol (1 ml/200 g body weight), and rats in the NC group were intragastrically administered distilled water (1 ml/200 g body weight). After the intragastric administration of ethanol for 1 h, the animals were anesthetized and gastric mucosal blood flow was measured. Serum were collected for ultra performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) metabolomics.RESULTS: There were no significant change in endogenous GLP-2 during gastric mucosal injury (P<0.05). Pretreatment with GLP-2 significantly reduced ethanol-induced gastric mucosal lesions by improving the gastric mucosal blood flow, as examined using a laser Doppler flow meter, Guth Scale, hematoxylin-eosin staining, and two-photon microscopy. UPLC-MS/MS analyses showed that GLP-2 also maintained a steady state of linoleic acid metabolism.CONCLUSIONS: Taken together, GLP-2 protects the gastric mucosa against ethanol-induced lesions by improving gastric mucosa blood flow and affecting linoleic acid metabolism.PMID:36589839 | PMC:PMC9801410 | DOI:10.3389/fendo.2022.1036559

Front Cell Dev Biol. 2022 Dec 15;10:1075810. doi: 10.3389/fcell.2022.1075810. eCollection 2022.ABSTRACTWe present the use of conductive spray polymer ionization mass spectrometry (CPSI-MS) combined with machine learning (ML) to rapidly gain the metabolic fingerprint from 1 μl liquid extraction from the biopsied tissue of triple-negative breast cancer (TNBC) in China. The 76 discriminative metabolite markers are verified at the primary carcinoma site and can also be successfully tracked in the serum. The Lasso classifier featured with 15- and 22-metabolites detected by CPSI-MS achieve a sensitivity of 88.8% for rapid serum screening and a specificity of 91.1% for tissue diagnosis, respectively. Finally, the expression levels of their corresponding upstream enzymes and transporters have been initially confirmed. In general, CPSI-MS/ML serves as a cost-effective tool for the rapid screening, diagnosis, and precise characterization for the TNBC metabolism reprogramming in the clinical practice.PMID:36589750 | PMC:PMC9798417 | DOI:10.3389/fcell.2022.1075810

Front Mol Biosci. 2022 Dec 15;9:1089359. doi: 10.3389/fmolb.2022.1089359. eCollection 2022.ABSTRACTNon-alcoholic fatty liver disease (NAFLD) has become one of the important causes of cirrhosis and liver cancer, resulting in a huge medical burden worldwide. Currently, effective non-invasive diagnostic indicators and drugs for NAFLD are still lacking. With the development of metabolomics technology, the changes in metabolites during the development of NAFLD have been gradually revealed. Bile acid (BA) is the main endpoint of cholesterol metabolism in the body. In addition, it also acts as a signaling factor to regulate metabolism and inflammation in the body through the farnesyl X receptor and G protein-coupled BA receptor. Studies have shown that BA metabolism is associated with the development of NAFLD, but a large number of animal and clinical studies are still needed. BA homeostasis is maintained through multiple negative feedback loops and the enterohepatic circulation of BA. Recently, treatment of NAFLD by interfering with BA synthesis and metabolism has become a new research direction. Here, we review the changes in BA metabolism and its regulatory mechanisms during the development of NAFLD and describe the potential of studies exploring novel non-invasive diagnostic indicators and therapeutic targets for NAFLD based on BA metabolism.PMID:36589245 | PMC:PMC9798289 | DOI:10.3389/fmolb.2022.1089359

Front Plant Sci. 2022 Dec 16;13:1075231. doi: 10.3389/fpls.2022.1075231. eCollection 2022.ABSTRACTThe present study aims to evaluate the response of the three Mediterranean local grapevines 'Garnacha Blanca', 'Garnacha Tinta', and 'Macabeo' to treatments with biocontrol products, namely a botanical extract (Akivi, Dittrichia viscosa extract) and a beneficial microorganism (Bacillus UdG, Bacillus velezensis). A combination of transcriptomics and metabolomics approaches were chosen in order to study grapevine gene expression and to identify gene marker candidates, as well as, to determine differentially concentrated grapevine metabolites in response to biocontrol product treatments. Grapevine plants were cultivated in greenhouse under controlled conditions and submitted to the treatments. Thereafter, leaves were sampled 24h after treatment to carry out the gene expression study by RT-qPCR for the three cultivars and by RNA-sequencing for 'Garnacha Blanca'. Differentially expressed genes (DEGs) were investigated for both treatments and highly influenced DEGs were selected to be tested in the three cultivars as treatment gene markers. In addition, the extraction of leaf components was performed to quantify metabolites, such as phytohormones, organic acids, and phenols. Considering the upregulated and downregulated genes and the enhanced metabolites concentrations, the treatments had an effect on jasmonic acid, ethylene, and phenylpropanoids defense pathways. In addition, several DEG markers were identified presenting a stable overexpression after the treatments in the three grapevine cultivars. These gene markers could be used to monitor the activity of the products in field treatments. Further research will be necessary to confirm these primary results under field conditions.PMID:36589113 | PMC:PMC9803176 | DOI:10.3389/fpls.2022.1075231

Front Plant Sci. 2022 Dec 14;13:1014396. doi: 10.3389/fpls.2022.1014396. eCollection 2022.ABSTRACTUniconazole, a triazole plant growth regulator, is widely used to regulate plant height and prevent the overgrowth of seedlings. However, the underlying molecular mechanism of uniconazole in inhibiting the hypocotyl elongation of seedlings is still largely unclear, and there has been little research on the integration of transcriptomic and metabolomic data to investigate the mechanisms of hypocotyl elonga-tion. Herein we observed that the hypocotyl elongation of flowering Chinese cabbage seedings was significantly inhibited by uniconazole. Interestingly, based on combined transcriptome and metabolome analyses, we found that the "phenylpropanoid biosynthesis" pathway was significantly affected by uniconazole. In this pathway, only one member of the portal enzyme gene family, named BrPAL4, was remarkably downregulated, which was related to lignin biosynthesis. Furthermore, the yeast one-hybrid and dual-luciferase assays showed that BrbZIP39 could directly bind to the promoter region of BrPAL4 and activate its transcript. The virus-induced gene silencing system further demonstrated that BrbZIP39 could positively regulate hypocotyl elongation and the lignin biosynthesis of hypocotyl. Our findings provide a novel insight into the molecular regulatory mechanism of uniconazole inhibiting hypocotyl elongation in flowering Chinese cabbage and confirm, for the first time, that uniconazole decreases lignin content through repressing the BrbZIP39-BrPAL4 module-mediated phenylpropanoid biosynthesis, which leads to the hypocotyl dwarfing of flowering Chinese cabbage seedlings.PMID:36589099 | PMC:PMC9794620 | DOI:10.3389/fpls.2022.1014396

Front Plant Sci. 2022 Dec 16;13:1065049. doi: 10.3389/fpls.2022.1065049. eCollection 2022.ABSTRACTPeanut testa (seed coat) contains large amounts of flavonoids that significantly influence seed color, taste, and nutritional qualities. There are various colors of peanut testa, however, their precise flavonoid components and regulatory mechanism of pigmentation remain unclear. In this study, a total of 133 flavonoids were identified and absolutely quantified in the seed coat of four peanut cultivars with different testa color using a widely targeted metabolomic approach. Black peanut skin had more types and substantial higher levels of cyanidin-based anthocyanins, which possibly contribute to its testa coloration. Procyanidins and flavan-3-ols were the major co-pigmented flavonoids in the red, spot and black peanuts, while flavanols were the most abundant constitutes in white cultivar. Although the concentrations as well as composition characteristics varied, the content ratios of procyanidins to flavan-3-ols were similar in all samples except for white peanut. Furthermore, MYB-like transcription factors, anthocyanidin reductases (ANR), and UDP-glycosyltransferases (UGT) were found to be candidate genes involved in testa pigmentation via RNA-seq and weighted gene co-expression network analysis. It is proposed that UGTs and ANR compete for the substrate cyanidin and the prevalence of UGTs activities over ANR one will determine the color pattern of peanut testa. Our results provide a comprehensive report examining the absolute abundance of flavonoid profiles in peanut seed coat, and the finding are expected to be useful for further understanding of regulation mechanisms of seed coat pigmentation in peanut and other crops.PMID:36589085 | PMC:PMC9800836 | DOI:10.3389/fpls.2022.1065049

Front Plant Sci. 2022 Dec 15;13:1101199. doi: 10.3389/fpls.2022.1101199. eCollection 2022.ABSTRACTAs a stem variety of lettuce, the fleshy stem is the main product organ of stem lettuce. The molecular mechanism of fleshy stem expansion in stem lettuce is a complex biological process. In the study, the material accumulation, gene expression, and morphogenesis during fleshy stem expansion process were analyzed by the comparative analysis of metabolome, transcriptome and the anatomical studies. The anatomical studies showed that the occurrence and activity of vascular cambium mainly led to the development of fleshy stems; and the volume of pith cells gradually increased and arranged tightly during the expansion process. A total of 822 differential metabolites and 9,383 differentially expressed genes (DEGs) were identified by the metabolomics and transcriptomics analyses, respectively. These changes significantly enriched in sugar synthesis, glycolysis, and plant hormone anabolism. The expression profiles of genes in the sugar metabolic pathway gradually increased in fleshy stem expansion process. But the sucrose content was the highest in the early stage of fleshy stem expansion, other sugars such as fructose and glucose content increased during fleshy stem expansion process. Plant hormones, including IAA, GA, CTK, and JA, depicted important roles at different stem expansion stages. A total of 1,805 DEGs were identified as transcription factors, such as MYB, bHLH, and bZIP, indicating that these transcription factor families might regulate the fleshy stems expansion in lettuce. In addition, the expression patterns identified by qRT-PCR were consistent with the expression abundance identified by the transcriptome data. The important genes and metabolites identified in the lettuce fleshy stem expansion process will provide important information for the further molecular mechanism study of lettuce fleshy stem growth and development.PMID:36589074 | PMC:PMC9798005 | DOI:10.3389/fpls.2022.1101199

Front Pharmacol. 2022 Dec 14;13:1040544. doi: 10.3389/fphar.2022.1040544. eCollection 2022.ABSTRACTThe alkylating antineoplastic agent cyclophosphamide (CP) is known to be toxic to the male reproductive system, but there are no effective prevention or treatment options. The flavonoid icariin (ICA), which is used in Chinese medicine, has been shown to have a number of biological functions, including testicular protection. The current study looked into the protective effects of ICA in preventing CP-induced spermatogenesis dysfunction. The current study looked into the role of ICA in preventing testicular dysfunction caused by CP. For 5 days, healthy adult mice were given saline or a single dose of CP (50 mg/kg) intraperitoneally (i.p). For the next 30 days, mice were given ICA (80 mg/kg) by gavage. Animals were euthanized 12 h after receiving ICA, and testes were removed for biochemical, histopathological, sperm evaluation, and transmission electron microscope analysis (TEM). We also investigated the potential biological effects of ICA on CP-induced spermatogenesis dysfunction in mice using an integrated proteomic and metabolomic approach. The levels of 8309 proteins and 600 metabolites were measured. The majority of the differential proteins and metabolites were found to be enriched in a variety of metabolic pathways, including the PI3K-Akt signaling pathway, necroptosis, the mTOR signaling pathway, glycerophospholipid metabolism, and ABC transporters, implying that ICA may have molecular mechanisms that contribute to CP-induced spermatogenesis dysfunction in the testis. Taken together, these findings show that ICA effectively reduces testis injury, implying that ICA may have a role in male infertility preservation.PMID:36588705 | PMC:PMC9794755 | DOI:10.3389/fphar.2022.1040544

Food Chem (Oxf). 2022 Dec 13;6:100157. doi: 10.1016/j.fochms.2022.100157. eCollection 2023 Jul 30.ABSTRACTThe objective of this study was to characterize the microbiota biodiversity of Uruçú-Amarela honey through metagenomics. Furthermore, the impact of maturation temperatures (20 and 30 °C) and time (0-180 days) on the physicochemical and antioxidant properties was investigated. 1H NMR was performed to verify metabolites formed during maturation. Uruçú-Amarela honey was mainly composed by lactic acid bacteria and osmophilic yeasts of genus Zygosaccharomyces. Maturation at 30 °C led to a higher fermentation activity, resulting in greater carbohydrate consumption, ethanol formation (0.0-0.6 %) and increased acidity (34.78-45.74 meq/kg) over the 180 days. It also resulted in honey with higher brown color (a* 0.7 to 3.89, b* 17.50-25.29) and antioxidant capacity, corroborating that the maturation is a suitable preservation technique for stingless bee honey, because it does not cause negative changes as it extends the shelf life of the stingless bee honey.PMID:36588603 | PMC:PMC9794890 | DOI:10.1016/j.fochms.2022.100157

J Anim Sci. 2023 Jan 2:skac427. doi: 10.1093/jas/skac427. Online ahead of print.ABSTRACTLiver abscesses in feedlot cattle are a polymicrobial infection with Fusobacterium necrophorum and Trueperella pyogenes as the primary and secondary etiologic agents, respectively. Cattle with liver abscesses do not exhibit clinical signs and the abscesses are detected only at slaughter. The objective was to conduct metabolomics analysis of purulent materials of liver abscesses to identify biochemicals. Liver abscesses from crossbred cattle (n=24) and Holstein steers (n=24), each fed high-grain finishing diet with tylosin (n=12) or no tylosin (n=12) were included in the study. Abscess purulent materials were analyzed by ultrahigh performance liquid chromatography-tandem mass spectroscopy. A total of 759 biochemicals were identified and were broadly categorized into carbohydrates, energy metabolism pathways intermediates, peptides, amino acids and their metabolites, lipids and their metabolites, nucleotides, vitamins and cofactors, xenobiotics, and partially characterized molecules. The top 50 biochemicals identified included amino acids, lipids, nucleotides, xenobiotics, peptides and carbohydrates and their metabolites. Among the 15 amino acid metabolites in the top-50 biochemicals, four were tryptophan metabolites, indoleacrylate, indolepropionate, tryptamine, and anthranilate. The 3-phenylpropionate, a product of phenylalanine metabolism, was the predominant metabolite in purulent materials. Between the four treatment groups, a two-way ANOVA analysis identified biochemicals that exhibited significant main effects for cattle type and in-feed tylosin use and their interactions. A total of 59 and 85 biochemicals were different (P < 0.05) between the cattle type (crossbred vs. Holstein steers) and in-feed tylosin use (tylosin vs. no tylosin), respectively. Succinate, an intermediate of lactate fermentation by some bacterial species, was one of the top 30 biochemicals that differentiated the four treatment groups. A number of lysophospholipids, indicative of bacterial and host cell membrane lyses, were identified in the purulent materials. In conclusion, to our knowledge this is the first report on the metabolome of liver abscess purulent materials and several biochemicals identified were related to metabolic activities of the bacterial community, particularly F. necrophorum and T. pyogenes. Biochemicals unique to liver abscesses that appear in the blood may serve as biomarkers and be of diagnostic value to detect liver abscesses of cattle before slaughter.PMID:36588460 | DOI:10.1093/jas/skac427

Mol Plant. 2022 Dec 31:S1674-2052(22)00476-2. doi: 10.1016/j.molp.2022.12.022. Online ahead of print.ABSTRACTKiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value, especially for the high content of vitamin C in fruit. Here, we de novo assembled two telomere-to-telomere kiwifruit genomes of A. chinensis var 'Donghong' (DH) and A. latifolia (KY), with total lengths of 608,327,852 bp and 640,561,626 bp for 29 chromosomes respectively. With burst of structural variants involving inversion, translocations and duplications within 8.39 million years, metabolite content of DH and KY exhibited differences including saccharides, lignans and vitamins. A regulatory ERF098 transcription factor family has expanded in KY and Actinidia. eriantha, both with ultra-high vitamin C content. With each assembly been phased into two complete haplotypes, we identified allelic variations between two sets of haplotypes, leading to protein sequence variations of 26,494 and 27,773 gene loci and allele specific expression (ASE) of 4,687 and 12,238 homozygous gene pairs. Synchronized metabolome and transcriptome changes during DH fruit development indicated the same dynamic patterns in expression and metabolite content levels, including free fatty acids and flavonols accumulated in the early stages, while sugar substances and amino acids in the late stages. An allele dominance AcSWEET9b gene was identified to positively correlate with high sucrose content in fruit. Compared to wild varieties and other Actinidia species, AcSWEET9b promoters were selected in red-flesh kiwifruits, facilitating the boost of fruit sucrose content, which probably explained why red-flesh kiwifruits are sweeter. These two gap-free kiwifruit genomes provide a valuable genetic basis for investigating mechanisms of domestication, opening up genome-based breeding era for kiwifruit.PMID:36588343 | DOI:10.1016/j.molp.2022.12.022

RNA Biol. 2023 Jan;20(1):186-197. doi: 10.1080/15476286.2023.2204586.ABSTRACTHere, we provide an in-depth analysis of the usefulness of single-sample metabolite/RNA extraction for multi-'omics readout. Using pulverized frozen livers of mice injected with lymphocytic choriomeningitis virus (LCMV) or vehicle (Veh), we isolated RNA prior (RNA) or following metabolite extraction (MetRNA). RNA sequencing (RNAseq) data were evaluated for differential expression analysis and dispersion, and differential metabolite abundance was determined. Both RNA and MetRNA clustered together by principal component analysis, indicating that inter-individual differences were the largest source of variance. Over 85% of LCMV versus Veh differentially expressed genes were shared between extraction methods, with the remaining 15% evenly and randomly divided between groups. Differentially expressed genes unique to the extraction method were attributed to randomness around the 0.05 FDR cut-off and stochastic changes in variance and mean expression. In addition, analysis using the mean absolute difference showed no difference in the dispersion of transcripts between extraction methods. Altogether, our data show that prior metabolite extraction preserves RNAseq data quality, which enables us to confidently perform integrated pathway enrichment analysis on metabolomics and RNAseq data from a single sample. This analysis revealed pyrimidine metabolism as the most LCMV-impacted pathway. Combined analysis of genes and metabolites in the pathway exposed a pattern in the degradation of pyrimidine nucleotides leading to uracil generation. In support of this, uracil was among the most differentially abundant metabolites in serum upon LCMV infection. Our data suggest that hepatic uracil export is a novel phenotypic feature of acute infection and highlight the usefulness of our integrated single-sample multi-'omics approach.PMID:37095747 | DOI:10.1080/15476286.2023.2204586

Best Pract Res Clin Gastroenterol. 2023 Feb-Mar;62-63:101830. doi: 10.1016/j.bpg.2023.101830. Epub 2023 Mar 16.ABSTRACTLifestyle modification is the primary intervention to control NAFLD progression, but despite evidence-based effectiveness it is difficult to distinguish the benefits of nutrition from physical activity and the optimal diet composition is not established. Macronutrients as saturated fatty acids, sugars and animal proteins are harmful in NAFLD and the Mediterranean Diet reducing sugar, red meat and refined carbohydrates and increasing unsaturated-fatty-acids was reported to be beneficial. However one size cannot fit all since NAFLD is a multifaceted syndrome encompassing many diseases of unknown etiologies, different clinical severity and outcomes. Studies of the intestinal metagenome, provided new insights into the physio-pathological interplay between intestinal microbiota and NAFLD. How much the microbiota heterogeneity can influence response to diet remains unknown. New knowledge indicates that AI guided personalized nutrition based on clinic-pathologic and genetic data combined with pre/post nutritional intervention gut metagenomics/metabolomics will be part of the future management of NAFLD.PMID:37094914 | DOI:10.1016/j.bpg.2023.101830

Methods Enzymol. 2023;683:153-170. doi: 10.1016/bs.mie.2022.08.039. Epub 2022 Nov 11.ABSTRACTMulti-omics has gained momentum over the past few years especially in plant single cell-type analysis as they aim to understand cellular molecular networks across different levels of genetic information flow. For multi-omics sample preparation, molecular extractions performed non-simultaneously create rooms for variation, inaccurate data, waste of limited samples, resources and labor. Here we optimized a protocol for 3-in-1 simultaneous extraction of RNA, metabolites, and proteins from the same single cell-type sample. We adapted a commercially available RNA kit with a few modifications to obtain high quality starting materials for sequencing and LC-MS/MS-based metabolomics and proteomics. RNAs are bound to the column, metabolites were extracted in a polar solvent and proteins are precipitated using acetone. This creates an all-in-one workflow using a standard RNA kit. Little training is required to carry out this protocol as it is simple and easy to use. It may be used with a wide range of plant species and different amounts of starting materials, including single cells.PMID:37087185 | DOI:10.1016/bs.mie.2022.08.039

Clin Transl Med. 2023 Jan;13(1):e1152. doi: 10.1002/ctm2.1152.ABSTRACTBACKGROUND: Gut-brain axis is widely implicated in the pathophysiology of Parkinson's disease (PD). We take an integrated approach to considering the gut as a target for disease-modifying intervention, using continuous measurements of disease facets irrespective of diagnostic divide.METHODS: We characterised 77 participants with diagnosed-PD, 113 without, by dietary/exogenous substance intake, faecal metabolome, intestinal inflammation, serum cytokines/chemokines, clinical phenotype including colonic transit time. Complete-linkage hierarchical cluster analysis of metabolites discriminant for PD-status was performed.RESULTS: Longer colonic transit was linked to deficits in faecal short-chain-fatty acids outside PD, to a 'tryptophan-containing metabolite cluster' overall. Phenotypic cluster analysis aggregated colonic transit with brady/hypokinesia, tremor, sleep disorder and dysosmia, each individually associated with tryptophan-cluster deficit. Overall, a faster pulse was associated with deficits in a metabolite cluster including benzoic acid and an imidazole-ring compound (anti-fungals) and vitamin B3 (anti-inflammatory) and with higher serum CCL20 (chemotactic for lymphocytes/dendritic cells towards mucosal epithelium). The faster pulse in PD was irrespective of postural hypotension. The benzoic acid-cluster deficit was linked to (well-recognised) lower caffeine and alcohol intakes, tryptophan-cluster deficit to higher maltose intake. Free-sugar intake was increased in PD, maltose intake being 63% higher (p = .001). Faecal calprotectin was 44% (95% CI 5%, 98%) greater in PD [p = .001, adjusted for proton-pump inhibitors (p = .001)], with 16% of PD-probands exceeding a cut-point for clinically significant inflammation compatible with inflammatory bowel disease. Higher maltose intake was associated with exceeding this calprotectin cut-point.CONCLUSIONS: Emerging picture is of (i) clinical phenotype being described by deficits in microbial metabolites essential to gut health; (ii) intestinal inflammation; (iii) a systemic inflammatory response syndrome.PMID:36588088 | DOI:10.1002/ctm2.1152