PubMed

Front Plant Sci. 2023 Jan 13;13:1049785. doi: 10.3389/fpls.2022.1049785. eCollection 2022.ABSTRACTPepper is one of the most vitamin C enriched vegetables worldwide. Although applying nitrogen (N) fertilizer is an important practice for high fruit yield in pepper production, it is still unclear how N application regulates pepper fruit vitamin C anabolism at different maturity stage. To further the understanding, we combined physiological and metabolomic analysis to investigate the fruit vitamin C content (including ascorbic acid (AsA) and dehydroascorbic acid (DHA)), related enzyme activity and non-targeted metabolites of field-grown chili pepper produced under different N levels at mature green and red stages. The results showed that increasing N application reduced AsA content in pepper fruit at both maturity stages, but highly elevated DHA content only at mature green stage. Regardless of N application level, AsA content displayed an increasing trend while DHA content was reduced as pepper fruit maturity advanced, resulting in a higher content of total vitamin C at the mature green stage. The L-galactose pathway, D-galacturonate pathway, and myo-inositol pathway were identified for AsA biosynthesis. The involved precursor metabolites were mainly negatively regulated by increasing N application, and their accumulation increased when pepper fruit developed from green to red stage. Meanwhile, the activities of key enzymes and metabolites in relation to degradation and recycling processes of AsA and DHA were increased or did not change with increasing N application, and they were differently influenced as fruit maturing. As a result, the recommended N application level (250 kg N ha-1) could maintain relatively high total vitamin C content in pepper fruits without yield loss at both maturity stages. These findings highlight the importance of optimizing N application level to maximize vitamin C content in pepper fruits, and provide a better understanding of the maturity stage-dependent N regulation on vitamin C anabolism.PMID:36714702 | PMC:PMC9880487 | DOI:10.3389/fpls.2022.1049785

3 Biotech. 2023 Feb;13(2):58. doi: 10.1007/s13205-023-03483-5. Epub 2023 Jan 24.ABSTRACTPisolithus albus is a ubiquitous ectomycorrhizal fungus that establishes symbiosis with a wide range of woody plants around the globe. The symbiotic association of this fungus plays a crucial role in the nutrient cycling of their host plants and enables them to thrive in adverse environmental conditions. Based on its ecological importance and lack of genomic studies, whole-genome sequencing was carried out to analyze P. albus sequences through an Illumina HiSeq X system. The functional annotations were performed against various databases to explore genomic patterns and traits possibly attributing to its specialization. Comparative genomics of P. albus with phylogenetically related Pisolithus microcarpus and Pisolithus tinctorius (only available genomes of Pisolithus at NCBI till now) led to the identification of their unique and shared basic functional and stress adaptation capabilities. The de novo assembled genome of 56.15 Mb with 91.8% BUSCO completeness is predicted to encode 23,035 genes. The study is aimed to generate solid genomic data resources for P. albus, forming the theoretical basis for future transcriptomic, proteomic and metabolomic studies.SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03483-5.PMID:36714549 | PMC:PMC9873894 | DOI:10.1007/s13205-023-03483-5

Front Physiol. 2023 Jan 13;13:994990. doi: 10.3389/fphys.2022.994990. eCollection 2022.ABSTRACTObjective: Menstrual disorders induced by high-temperature environments, can seriously damage women's reproductive health and workability. The regulation mechanism underlying it is not yet to be elucidated. Saliva is an information-rich biological fluid that can reflect systemic diseases. Here, we investigated the characteristics of menstrual cycle disorders and saliva metabolomics to provide a deeper insight of the regulation mechanism of young women in high-temperature environments. Methods: Women from high and normal temperature areas of China were selected and divided into two groups-high-temperature (H group) and control (C group). A questionnaire survey was conducted in summer (July) to investigate the incidence rate of menstrual disorders, characteristics of the disorders, and factors influencing the risk of these disorders in different regions. Metabolomics was applied to analyze the characteristics of the salivary metabolites and neurotransmitters in the two groups of women with menstrual disorders. Results: The incidence rate of menstrual disorders was significantly higher in the H group than that in the C group (p < 0.05). High-temperature environment, stress, and sleep quality were identified as critical factors associated with menstrual disorders. Non-targeted saliva metabolomics identified 64 significantly different metabolites between two groups, which mainly enriched in metabolic pathways such as carbohydrate metabolism, membrane transport, digestive system, and nucleotide metabolism (p < 0.05). N-acetylneuraminic acid, MYO, and tyramine may be candidate markers for early diagnosis of menstrual disorders in high temperature environments. Metabolites may be involving in the acute-phase response during an inflammatory process, to affecting the reproductive system by influencing the HPA axis loop. Regulations about oocyte membrane production and the luteal functions would be exerted in menstrual disorders. Targeted metabolomics of neurotransmitters revealed increased expression of histamine (HA) and glutamine and decreased expression of 5-hydroxyindole acetic acid (5-HIAA) (p < 0.05). Conclusion: Menstrual disorder characteristics induced by high temperature environments were specific. Anxiety, sleep quality and temperature feeling were the key factors to the menstrual disorder. endocrine regulation mechanism and inflammatory reactions might contribute to the development of menstrual disorders through influencing the formation of the follicular cell membrane.PMID:36714308 | PMC:PMC9880290 | DOI:10.3389/fphys.2022.994990

Biomed Res Int. 2023 Jan 18;2023:7407772. doi: 10.1155/2023/7407772. eCollection 2023.ABSTRACTIris bulleyana Dykes (Southwest iris) is an extensively distributed Iridaceae species with blue or white flowers. Hereby, we performed a systematic study, employing metabolomics and transcriptomics to uncover the subtle color differentiation from blue to white in Southwest iris. Fresh flower buds from both cultivars were subjected to flavonoid/anthocyanin and carotenoid-targeted metabolomics along with transcriptomic sequencing. Among 297 flavonoids, 24 anthocyanins were identified, and 13 showed a strong down-accumulation pattern in the white flowers compared to the blue flowers. Significant downregulation of 3GT and 5GT genes involved in the glycosylation of anthocyanins was predicted to hinder the accumulation of anthocyanins, resulting in white coloration. Besides, no significant altered accumulation of carotenoids and expression of their biosynthetic genes was observed between the two cultivars. Our study systematically addressed the color differentiation in I. bulleyana flowers, which can aid future breeding programs.PMID:36714023 | PMC:PMC9876678 | DOI:10.1155/2023/7407772

Biomed Res Int. 2023 Jan 19;2023:9862038. doi: 10.1155/2023/9862038. eCollection 2023.ABSTRACT[This retracts the article DOI: 10.1155/2022/5162845.].PMID:36714022 | PMC:PMC9879685 | DOI:10.1155/2023/9862038

Mass Spectrom (Tokyo). 2022;11(1):A0112. doi: 10.5702/massspectrometry.A0112. Epub 2022 Dec 29.ABSTRACTProton-transfer-reaction (PTR) mass spectrometry (MS), a widely used method for detecting trace-levels of volatile organic compounds in gaseous samples, can also be used for the analysis of small non-volatile molecules by using supercritical fluid as a transporter for the molecules. Supercritical fluid extraction (SFE) is a method that permits lipophilic compounds to be rapidly and selectively extracted from complex matrices. The combination of the high sensitivity of PTR MS with the SFE is a potentially novel method for analyzing small molecules in a single cell, particularly for the analysis of lipophilic compounds. We preliminarily evaluated this method for analyzing the components of a single HeLa cell that is fixed on a stainless steel frit and is then directly introduces the SFE extracts into the PTR MS. A total of 200/91 ions were observed in positive/negative ion mode time-of-flight mass spectra, and the masses of 11/10 ions could be matched to chemical formulae obtained from the LipidMaps lipids structure database. Using various authentic lipophilic samples, the method could be used to detect free fatty acids in the sub-femtomole to femtomole order in the negative ion mode, the femtomole to sub-picomole order for fat-soluble vitamins, and the picomole order for poly aromatic hydrocarbons in both the positive and negative ion mode.PMID:36713805 | PMC:PMC9853953 | DOI:10.5702/massspectrometry.A0112

Mass Spectrom (Tokyo). 2022;11(1):A0106. doi: 10.5702/massspectrometry.A0106. Epub 2022 Dec 15.ABSTRACTIn metabolomics studies using high-resolution mass spectrometry (MS), a set of product ion spectra is comprehensively acquired from observed ions using the data-dependent acquisition (DDA) mode of various tandem MS. However, especially for low-intensity signals, it is sometimes difficult to distinguish artifact signals from true fragment ions derived from a precursor ion. Inadequate precision in the measured m/z value is also one of the bottlenecks to narrowing down the candidate compositional formula. In this study, we report that averaging multiple product ion spectra can improve m/z precision as well as the reliability of fragment ions that are observed in such spectra. A graph-based method was applied to cluster a set of similar spectra from multiple DDA data files resulting in creating an averaged product-ion spectrum. The error levels for the m/z values declined following the central limit theorem, which allowed us to reduce the number of candidate compositional formulas. The improved reliability and precision of the averaged spectra will contribute to a more efficient annotation of product ion spectral data.PMID:36713802 | PMC:PMC9853114 | DOI:10.5702/massspectrometry.A0106

Front Oncol. 2023 Jan 11;12:1110104. doi: 10.3389/fonc.2022.1110104. eCollection 2022.ABSTRACTPURPOSE: In metastatic colorectal cancer (mCRC) patients (pts), treatment strategies integrating liver resection with induction chemotherapy offer better 5-year survival rates than chemotherapy alone. However, liver resection is a complex and costly procedure, and recurrence occurs in almost 2/3rds of pts, suggesting the need to identify those at higher risk. The aim of this work was to evaluate whether the integration of plasma metabolomics and lipidomics combined with the multiplex analysis of a large panel of plasma cytokines can be used to predict the risk of relapse and other patient outcomes after liver surgery, beyond or in combination with clinical morphovolumetric criteria.EXPERIMENTAL DESIGN: Peripheral blood metabolomics and lipidomics were performed by 600 MHz NMR spectroscopy on plasma from 30 unresectable mCRC pts treated with bevacizumab plus oxaliplatin-based regimens within the Obelics trial (NCT01718873) and subdivided into responder (R) and non-R (NR) according to 1-year disease-free survival (DFS): ≥ 1-year (R, n = 12) and < 1-year (NR, n = 18). A large panel of cytokines, chemokines, and growth factors was evaluated on the same plasma using Luminex xMAP-based multiplex bead-based immunoassay technology. A multiple biomarkers model was built using a support vector machine (SVM) classifier.RESULTS: Sparse partial least squares discriminant analysis (sPLS-DA) and loading plots obtained by analyzing metabolomics profiles of samples collected at the time of response evaluation when resectability was established showed significantly different levels of metabolites between the two groups. Two metabolites, 3-hydroxybutyrate and histidine, significantly predicted DFS and overall survival. Lipidomics analysis confirmed clear differences between the R and NR pts, indicating a statistically significant increase in lipids (cholesterol, triglycerides and phospholipids) in NR pts, reflecting a nonspecific inflammatory response. Indeed, a significant increase in proinflammatory cytokines was demonstrated in NR pts plasma. Finally, a multiple biomarkers model based on the combination of presurgery plasma levels of 3-hydroxybutyrate, cholesterol, phospholipids, triglycerides and IL-6 was able to correctly classify patients by their DFS with good accuracy.CONCLUSION: Overall, this exploratory study suggests the potential of these combined biomarker approaches to predict outcomes in mCRC patients who are candidates for liver metastasis resection after induction treatment for defining personalized management and treatment strategies.PMID:36713567 | PMC:PMC9875807 | DOI:10.3389/fonc.2022.1110104

Front Immunol. 2023 Jan 12;13:1020844. doi: 10.3389/fimmu.2022.1020844. eCollection 2022.ABSTRACTBACKGROUND: The new types of mRNA-containing lipid nanoparticle vaccines BNT162b2 and mRNA-1273 and the adenovirus-based vaccine AZD1222 were developed against SARS-CoV-2 and code for its spike (S) protein. Several studies have investigated short-term antibody (Ab) responses after vaccination.OBJECTIVE: However, the impact of these new vaccine formats with unclear effects on the long-term Ab response - including isotype, subclass, and their type of Fc glycosylation - is less explored.METHODS: Here, we analyzed anti-S Ab responses in blood serum and the saliva of SARS-CoV-2 naïve and non-hospitalized pre-infected subjects upon two vaccinations with different mRNA- and adenovirus-based vaccine combinations up to day 270.RESULTS: We show that the initially high mRNA vaccine-induced blood and salivary anti-S IgG levels, particularly IgG1, markedly decrease over time and approach the lower levels induced with the adenovirus-based vaccine. All three vaccines induced, contrary to the short-term anti-S IgG1 response with high sialylation and galactosylation levels, a long-term anti-S IgG1 response that was characterized by low sialylation and galactosylation with the latter being even below the corresponding total IgG1 galactosylation level. Instead, the mRNA, but not the adenovirus-based vaccines induced long-term IgG4 responses - the IgG subclass with inhibitory effector functions. Furthermore, salivary anti-S IgA levels were lower and decreased faster in naïve as compared to pre-infected vaccinees. Predictively, age correlated with lower long-term anti-S IgG titers for the mRNA vaccines. Furthermore, higher total IgG1 galactosylation, sialylation, and bisection levels correlated with higher long-term anti-S IgG1 sialylation, galactosylation, and bisection levels, respectively, for all vaccine combinations.CONCLUSION: In summary, the study suggests a comparable "adjuvant" potential of the newly developed vaccines on the anti-S IgG Fc glycosylation, as reflected in relatively low long-term anti-S IgG1 galactosylation levels generated by the long-lived plasma cell pool, whose induction might be driven by a recently described TH1-driven B cell response for all three vaccines. Instead, repeated immunization of naïve individuals with the mRNA vaccines increased the proportion of the IgG4 subclass over time which might influence the long-term Ab effector functions. Taken together, these data shed light on these novel vaccine formats and might have potential implications for their long-term efficacy.PMID:36713457 | PMC:PMC9877300 | DOI:10.3389/fimmu.2022.1020844

Front Immunol. 2023 Jan 13;13:1089987. doi: 10.3389/fimmu.2022.1089987. eCollection 2022.ABSTRACTINTRODUCTION: The integrity of the gut barrier (GB) is fundamental to regulate the crosstalk between the microbiota and the immune system and to prevent inflammation and autoimmunity at the intestinal level but also in organs distal from the gut such as the pancreatic islets. In support to this idea, we recently demonstrated that breakage of GB integrity leads to activation of islet-reactive T cells and triggers autoimmune Type 1 Diabetes (T1D). In T1D patients as in the NOD mice, the spontaneous model of autoimmune diabetes, there are alterations of the GB that specifically affect structure and composition of the mucus layer; however, it is yet to be determined whether a causal link between breakage of the GB integrity and occurrence of autoimmune T1D exists.METHODS: Here we restored GB integrity in the NOD mice through administration of an anti-inflammatory diet (AID- enriched in soluble fiber inulin and omega 3-PUFA) and tested the effect on T1D pathogenesis.RESULTS: We found that the AID prevented T1D in NOD mice by restoring GB integrity with increased mucus layer thickness and higher mRNA transcripts of structural (Muc2) and immunoregulatory mucins (Muc1 and Muc3) as well as of tight junction proteins (claudin1). Restoration of GB integrity was linked to reduction of intestinal inflammation (i.e., reduced expression of IL-1β, IL-23 and IL-17 transcripts) and expansion of regulatory T cells (FoxP3+ Treg cells and IL-10+ Tr1 cells) at the expenses of effector Th1/Th17 cells in the intestine, pancreatic lymph nodes (PLN) and intra-islet lymphocytes (IIL) of AID-fed NOD mice. Importantly, the restoration of GB integrity and immune homeostasis were associated with enhanced concentrations of anti-inflammatory metabolites of the ω3/ω6 polyunsaturated fatty acids (PUFA) and arachidonic pathways and modifications of the microbiome profile with increased relative abundance of mucus-modulating bacterial species such as Akkermansia muciniphila and Akkermansia glycaniphila.DISCUSSION: Our data provide evidence that the restoration of GB integrity and intestinal immune homeostasis through administration of a tolerogenic AID that changed the gut microbial and metabolic profiles prevents autoimmune T1D in preclinical models.PMID:36713378 | PMC:PMC9880528 | DOI:10.3389/fimmu.2022.1089987

Front Microbiol. 2023 Jan 11;13:957830. doi: 10.3389/fmicb.2022.957830. eCollection 2022.ABSTRACTBACKGROUND: Chronic obstructive pulmonary disease (COPD) collectively refers to chronic and progressive lung diseases that cause irreversible limitations in airflow. Patients with COPD are at high risk for severe respiratory symptoms upon influenza virus infection. Airway epithelial cells provide the first-line antiviral defense, but whether or not their susceptibility and response to influenza virus infection changes in COPD have not been elucidated. Therefore, this study aimed to compare the susceptibility of COPD- and control-derived airway epithelium to the influenza virus and assess protein changes during influenza virus infection by quantitative proteomics.MATERIALS AND METHODS: The presence of human- and avian-type influenza A virus receptor was assessed in control and COPD lung sections as well as in fully differentiated primary human bronchial epithelial cells (phBECs) by lectin- or antibody-based histochemical staining. PhBECs were from COPD lungs, including cells from moderate- and severe-stage diseases, and from age-, sex-, smoking, and history-matched control lung specimens. Protein profiles pre- and post-influenza virus infection in vitro were directly compared using quantitative proteomics, and selected findings were validated by qRT-PCR and immunoblotting.RESULTS: The human-type influenza receptor was more abundant in human airways than the avian-type influenza receptor, a property that was retained in vitro when differentiating phBECs at the air-liquid interface. Proteomics of phBECs pre- and post-influenza A virus infection with A/Puerto Rico/8/34 (PR8) revealed no significant differences between COPD and control phBECs in terms of flu receptor expression, cell type composition, virus replication, or protein profile pre- and post-infection. Independent of health state, a robust antiviral response to influenza virus infection was observed, as well as upregulation of several novel influenza virus-regulated proteins, including PLSCR1, HLA-F, CMTR1, DTX3L, and SHFL.CONCLUSION: COPD- and control-derived phBECs did not differ in cell type composition, susceptibility to influenza virus infection, and proteomes pre- and post-infection. Finally, we identified novel influenza A virus-regulated proteins in bronchial epithelial cells that might serve as potential targets to modulate the pathogenicity of infection and acute exacerbations.PMID:36713229 | PMC:PMC9875134 | DOI:10.3389/fmicb.2022.957830

Front Microbiol. 2023 Jan 13;13:1054612. doi: 10.3389/fmicb.2022.1054612. eCollection 2022.ABSTRACTINTRODUCTION: This study aimed to investigate the effects of different growth stages (booting period-SYK; initial flowering-SCK; full flowering-SSK) on the fermentation quality, microbial community, metabolic pathways and metabolomic characteristics of Italian ryegrass silage.METHODS: Single molecule real-time (SMRT) sequencing and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) were used to analyze bacterial communities and metabolites, respectively.RESULTS: After 60 d of fermentation, SYK had the lowest pH and the highest lactic acid content, which were significantly different from the other groups. The bacteria with the highest abundance in SYK, SCK and SSK groups were Lactiplantibacillus plantarum (63.98%), Weissella minor (28.82%) and Levilactobacillus brevis (64.81%), respectively. In addition, among the main differential metabolites in different growth stages, the number of amino acids was the most, and the corresponding metabolic pathways were mainly amino acid metabolic pathways. The biosynthesis of phenylalanine, tyrosine and tryptophan was significantly enriched (p<0.01) at booting stage and full flowering stage. Purine metabolism and ABC transporter pathway were significantly enriched at the initial flowering (p<0.001). Lactiplantibacillus plantarum had a negative correlation with xanthine and ganoderic acid F. Weissella minor had a positive correlation with D-Mannose and ganoderic acid F. Levilactobacillus brevis had a positive correlation with xanthine, and Latilactobacillus sakei had a positive correlation with cinnamic acid, D-Mannose, 2-Hydroxycinnamic acid and uridine.DISCUSSION: In conclusion, this study reveals the interaction mechanisms between ryegrass raw materials at different growth stages and epiphytic microorganisms during ensiling fermentation, providing new ideas for screening functional lactic acid bacteria, and laying a theoretical foundation for the production of safe and high-quality silage.PMID:36713224 | PMC:PMC9880220 | DOI:10.3389/fmicb.2022.1054612

Front Microbiol. 2023 Jan 13;13:1101144. doi: 10.3389/fmicb.2022.1101144. eCollection 2022.ABSTRACTBacillus subtilis DE111® is a safe, well-tolerated commercially available spore-forming probiotic that has been clinically shown to support a healthy gut microbiome, and to promote digestive and immune health in both adults and children. Recently it was shown that this spore-forming probiotic was capable of germinating in the gastrointestinal tract as early as 3 h after ingestion. However, a better understanding of the mechanisms involved in the efficacy of DE111® is required. Therefore, the present investigation was undertaken to elucidate the functional properties of DE111® through employing a combination of in vitro functional assays and genome analysis. DE111® genome mining revealed the presence of several genes encoding acid and stress tolerance mechanisms in addition to adhesion proteins required to survive and colonize harsh gastrointestinal environment including multi subunit ATPases, arginine deiminase (ADI) pathway genes (argBDR), stress (GroES/GroEL and DnaK/DnaJ) and extracellular polymeric substances (EPS) biosynthesis genes (pgsBCA). DE111® harbors several genes encoding enzymes involved in the metabolism of dietary molecules (protease, lipases, and carbohyrolases), antioxidant activity and genes associated with the synthesis of several B-vitamins (thiamine, riboflavin, pyridoxin, biotin, and folate), vitamin K2 (menaquinone) and seven amino acids including five essential amino acids (threonine, tryptophan, methionine, leucine, and lysine). Furthermore, a combined in silico analysis of bacteriocin producing genes with in vitro analysis highlighted a broad antagonistic activity of DE111® toward numerous urinary tract, intestinal, and skin pathogens. Enzymatic activities included proteases, peptidases, esterase's, and carbohydrate metabolism coupled with metabolomic analysis of DE111® fermented ultra-high temperature milk, revealed a high release of amino acids and beneficial short chain fatty acids (SCFAs). Together, this study demonstrates the genetic and phenotypic ability of DE111® for surviving harsh gastric transit and conferring health benefits to the host, in particular its efficacy in the metabolism of dietary molecules, and its potential to generate beneficial SCFAs, casein-derived bioactive peptides, as well as its high antioxidant and antimicrobial potential. Thus, supporting the use of DE111® as a nutrient supplement and its pottential use in the preparation of functional foods.PMID:36713219 | PMC:PMC9880548 | DOI:10.3389/fmicb.2022.1101144

Front Microbiol. 2023 Jan 12;13:1076577. doi: 10.3389/fmicb.2022.1076577. eCollection 2022.ABSTRACTMany active metabolites have been identified from various species of the fungal genus Cordyceps. A predominant species of this genus is Cordyceps gunnii, but there are limited reports on the active ingredients from this species. This study aimed to conduct activity assays and metabolome analysis on extracts of C. gunnii obtained under different culture conditions. Five different solid media were selected to culture the mycelium of C. gunnii and the metabolites were extracted with organic solvents; concurrently, the wild stroma and host complexes of C. gunnii were extracted by ethyl acetate. Extracts were subsequently assayed for various biological activities and were analyzed by untargeted metabolomics. There were significant differences in the activities and metabolites of C. gunnii extracts from different culture conditions and from wild stroma and host complexes. The extracts of stroma and host complexes and mycelia cultured on WGA medium for 21 days exhibited similar effective inhibitory activity against five cell lines. A total of 51 metabolites were annotated and included various structural types. The literatures indicate that most of the identified compounds have a variety of different biological activities. These findings provide the basis for further systematic excavation of C. gunnii and improved utilization of this fungal species.PMID:36713217 | PMC:PMC9878563 | DOI:10.3389/fmicb.2022.1076577

Front Microbiol. 2023 Jan 11;13:1113050. doi: 10.3389/fmicb.2022.1113050. eCollection 2022.ABSTRACTINTRODUCTION: Nettle is kind of new feed resources and benefit for animal production. However, a few studies observed that quality of nettle silage was poor under naturally fermentation. Consider of microbial activity was the mainly factors for fermentation characteristics of silage.METHODS: Thus, the present study investigated the potential factors causing nettle silage failure through metabolome and bacterial community composition analyses during ensiling.RESULTS: During ensiling, the pH was >6.22, and water-soluble carbohydrate and organic acid contents stabilized after 7 d. At the genus level, Enterococcus, Weissella, and Pediococcus were the dominant bacteria (relative abundance were 30.06-39.39, 17.29-23.34, and 3.13-7.22%, respectively), with stable trends, whereas Lactococcus and Enterobacter relative abundance decreased significantly over time (relative abundance were 5.68-13.96 and 3.86-24.1%, respectively). Lactobacillus relative abundance was <1% during the entire ensiling period, and malic acid metabolic pathway was the most important pathway. Enterococcus, Pediococcus, and Weissella were negatively correlated with malic acid, with Lactobacillus displaying an opposite trend.DISCUSSION: The results suggested that Lactobacillus activity was the lowest among lactic acid bacteria (LAB) during ensiling, which is the main reason for nettle ensiling failure, and attributable to a low capacity to compete for fermentation substrates such as malic acid against other LAB during ensiling. Additionally, anti-bacteria activity of nettle probably inhibited Enterobacter activity during ensiling. Present study probably given a solution for improve nettle silage quality through addition with malic acid.PMID:36713207 | PMC:PMC9876617 | DOI:10.3389/fmicb.2022.1113050

Front Microbiol. 2023 Jan 13;13:1082835. doi: 10.3389/fmicb.2022.1082835. eCollection 2022.ABSTRACTColorectal cancer (CRC) is a common malignancy worldwide, and the gut microbiota and metabolites play an important role in its initiation and progression. In this study, we constructed a mouse model of inflammation-induced colorectal tumors, with fixed doses of azoxymethane/dextran sulfate sodium (AOM/DSS). We found that colorectal tumors only formed in some mice treated with certain concentrations of AOM/DSS (tumor group), whereas other mice did not develop tumors (non-tumor group). 16S rDNA amplicon sequencing and liquid chromatography-mass spectrometry (LC-MS)/MS analyses were performed to investigate the microbes and metabolites in the fecal samples. As a result, 1189 operational taxonomic units (OTUs) were obtained from the fecal samples, and the non-tumor group had a relatively higher OTU richness and diversity. Moreover, 53 different microbes were identified at the phylum and genus levels, including Proteobacteria, Cyanobacteria, and Prevotella. Furthermore, four bacterial taxa were obviously enriched in the non-tumor group, according to linear discriminant analysis scores (log10) > 4. The untargeted metabolomics analysis revealed significant differences between the fecal samples and metabolic phenotypes. Further, the heatmaps and volcano plots revealed 53 and 19 dysregulated metabolites between the groups, in positive and negative ion modes, respectively. Styrene degradation and amino sugar-nucleotide sugar metabolism pathways were significantly different in positive and negative ion modes, respectively. Moreover, a correlation analysis between the metabolome and microbiome was further conducted, which revealed the key microbiota and metabolites. In conclusion, we successfully established a tumor model using a certain dose of AOM/DSS and identified the differential intestinal microbiota and characteristic metabolites that might modulate tumorigenesis, thereby providing new concepts for the prevention and treatment of CRC.PMID:36713186 | PMC:PMC9880073 | DOI:10.3389/fmicb.2022.1082835

Front Pharmacol. 2023 Jan 11;13:1104954. doi: 10.3389/fphar.2022.1104954. eCollection 2022.ABSTRACTIntroduction: Alpiniae oxyphyllae Fructus (AOF) has been abundantly utilized for the treatment of diarrhea, dyspepsia, kidney asthenia, and abdominal pain in China. AOF is effective for treating AD in clinical trials, but its exact mode of action is yet unknown. Methods: In this study, metabolomics was combined to ascertain the alterations in plasma metabolism in APP/PS1 transgenic mice, the therapy of AOF on model mice, and the dynamic variations in 15 bile acids (BAs) concentration. Results: 31 differential biomarkers were finally identified in APP/PS1 group vs. the WT group. The levels of 16 metabolites like sphinganine (Sa), lyso PE (20:2), lysoPC (17:0), glycocholic acid (GCA), deoxycholicacid (DCA) were increased in APP/PS1 group, and those of 15 metabolites like phytosphingosine, cer (d18:0/14:0), and fumaric acid were reduced in APP/PS1 group. After AOF treatment, 29 of the 31 differential metabolites showed a tendency to be back-regulated, and 15 metabolites were significantly back-regulated, including sphinganine (Sa), lyso PE (20:2), glycocholic acid (GCA), deoxycholic acid (DCA). The relationship between BAs level and AD had been received increasing attention in recent years, and we also found notable differences between DCA and GCA in different groups. Therefore, a BAs-targeted metabonomic way was established to determine the level of 15 bile acids in different groups. The consequence demonstrated that primary BAs (CA, CDCA) declined in APP/PS1 model mice. After 3 months of AOF administration, CA and CDCA levels showed an upward trend. Conjugated primary bile acids (TCA, GCA, TCDCA, GCDCA), and secondary bile acids (DCA, LCA, GDCA, TDCA, TLCA GLCA) ascended in APP/PS1 group. After 3 months of AOF treatment, the levels of most BAs decreased to varying degrees. Notably, the metabolic performance of DCA and GCA in different groups was consistent with the predictions of untargeted metabolomics, validating the correctness of untargeted metabolomics. Discussion: According to metabolic pathways of regulated metabolites, it was prompted that AOF ameliorated the symptom of AD mice probably by regulating bile acids metabolism. This study offers a solid foundation for further research into the AOF mechanism for the therapy of AD.PMID:36712678 | PMC:PMC9873993 | DOI:10.3389/fphar.2022.1104954

Front Nutr. 2023 Jan 11;9:1095483. doi: 10.3389/fnut.2022.1095483. eCollection 2022.ABSTRACTTo study the prevention and mechanism of oat antimicrobial peptides (AMPs) on enteritis. Oat protein was hydrolyzed by alkaline protease and isolated to obtain oat antimicrobial peptides. Rat enteritis models were constructed using dextran sodium sulfate (DSS), and a blank group, a negative control group, a positive control group, and an experimental group (low dose, medium dose, and high dose) were established. Through pathological test, antioxidant test, intestinal microbial and metabolite determination, it was found that AMPS can improve the antioxidant capacity of colon, reduce the production of inflammatory cells, and have the effect of preventing enteritis. In addition, the AMPS group is able to change and reduce the abundance of Bacteroides-eggerthii-DSM-20697 and Desulfovibrionaceae, increase the abundance of probiotics such as roboutsia and Ruminococcus and optimize the diversity of intestinal microorganisms. Then, the combined analysis of microorganism and metabolites showed that Romboutsia and Ruminococcus reduced the contents of amino acid and glucose and promoted the production of phospholipid, while Bacteroides promoted the synthesis of amino acid in the body. From the above, it can be seen that DSS causes damage to the mechanical barrier of the gut. Oat antimicrobial peptides provide a microbial barrier for the gut microbes, which produce acetic acid and succinic acid with small amounts of isobutyric acid, isovaleric acid, and lactic acid. The acidic metabolites produced reduce the pH of the gut and produce substances with antibacterial effects (such as lipophilic molecules, antibiotics, and hydroperoxides). Inhibit the growth and reproduction of other harmful bacteria, Vibrio desulphuris, from adhering to and colonizing the intestinal mucosa. Secreted short-chain fatty acids, such as acetate and butyric acid, maintain tight connections between the epithelial cells of the intestinal mucosa, thus protecting the mechanical barrier of the intestinal mucosa. Moreover, amino acids are converted into phospholipid metabolism through protein digestion and absorption to promote the production of phospholipid in the intestine and repair damaged cell membranes.PMID:36712538 | PMC:PMC9875082 | DOI:10.3389/fnut.2022.1095483

Front Nutr. 2023 Jan 11;9:1111283. doi: 10.3389/fnut.2022.1111283. eCollection 2022.ABSTRACTOBJECTIVES: Lotus root (Nelumbo nucifera Gaertn) is a common medicinal-food dual-use vegetable. In this study, the effects of lotus root extract on acute alcoholism were investigated.METHODS: The Walle-Hoch method was used to determine the ADH activity of lotus root extracts in vitro. Lotus root methanol extract were identified by UPLC-QTOF-MS/MS based metabolomics analysis. Then 109 active ingredients with achievable oral doses and drug-like properties were explored using the TCMSP platform. SwissTargetPrediction Database to predict lotus root treatment targets for acute alcoholismSTRING database (https://www.string-db.org/) was used to construct protein-protein interaction network graphs. Gene ontology (GO) functional, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of genes common to lotus root and alcoholism by Metascap database. Molecular docking simulations were performed using AutoDock 1.5.6 software. Animal experiments verified the relieving effect of lotus root extract on acute alcoholism after intervention.RESULTS: Results indicated the methanol extract of lotus root showed the highest activation rate of ethanol dehydrogenase in vitro (18.87%). The 433 compounds of lotus root methanol extract were identified by UPLC-QTOF-MS/MS based metabolomics analysis. Bioinformatics analysis indicate that there were 224 intersectioning targets between lotus root extract and acute alcoholism. KEGG enrichment analysised shows that lotus root extract may play a role in treating acute alcoholism by intervening with the neuroactive ligand-receptor interaction pathway. The protein-protein interaction network (PPI) analysis found that HSP90AA1, MAPK1 and STAT3 played a key role in lotus root extract-modulated PPI networks. Molecular docking showed that (7R, 8S)-dihydrodihydrodipine cypressol had the best binding ability with MAPK1. Experiments in mice indicate that lotus root extract improved the activity of liver alcohol dehydrogenase (ADH), acetaldehyde dehydrogenase (ALDH), catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX), increase glutathione (GSH) and reduce malondialdehyde (MDA) levels, decrease glutamate transaminase (AST), alanine transaminase (ALT) and alkaline phosphatase (AKP) in the serum of mice with acute alcoholism, and accelerate the metabolic rate of alcohol after drinking. This study reveals the mechanism of lotus root to alleviate acute alcoholism, which provides a basis for further research on functional foods using lotus root and offers new possibilities for the treatment of acute alcoholism.CONCLUSIONS: The results of the current study showed that the methanolic extract of lotus root had the highest activation rate of ethanol dehydrogenase. Network pharmacology results suggest that lotus root extract may play a role in the treatment of alcoholism by regulating signaling pathways, such as neuroactive ligand-receptor interactions, as well as biological processes, such as regulation of secretion, regulation of ion transport, response to lipopolysaccharides, and response to alcohol. Animal experiments confirmed the therapeutic effect of lotus root on acute alcoholism mechanistically through activation of alcohol catabolic enzyme, reduction of oxidative stress and protection of liver function.PMID:36712522 | PMC:PMC9875029 | DOI:10.3389/fnut.2022.1111283

PNAS Nexus. 2022 Nov 16;1(5):pgac257. doi: 10.1093/pnasnexus/pgac257. eCollection 2022 Nov.ABSTRACTMicrobial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.PMID:36712343 | PMC:PMC9802219 | DOI:10.1093/pnasnexus/pgac257