Amino Acid Synthesis Pathways Research Articles

Glyphosate Herbicide Impacts on the Seagrasses Halodule wrightii and Ruppia maritima from a Subtropical Florida Estuary

Seagrass meadows are among the most threatened ecosystems on Earth, with losses attributed to increasing coastal populations, degraded water quality and climate change. As coastal communities work to improve water quality, there is increased concern regarding the use of herbicides within the watersheds of these sensitive ecosystems. Glyphosate is the most widely used herbicide on Earth because it is non-selective and lethal to most plants. Also, the targeted amino acid synthesis pathway of glyphosate is not carried out by vertebrates, and it is generally considered one of the safer but effective herbicides on the market. At least partially due to its cost-effectiveness compared to other techniques, including mechanical harvesting, glyphosate use in the aquatic environment has increased in coastal areas to manage aquatic weeds, maintain navigable waterways and mitigate upland flooding. This has prompted concerns regarding potential ecosystem-level impacts. To test the acute toxicity of glyphosate to seagrasses, mesocosm experiments exposed Ruppia maritima and Halodule wrightii to 1 ppm, 100 ppm and 1000 ppm of glyphosate (as glyphosate acid). No significant decrease in leaf chlorophyll a (Chl a) was identified for either species at 1 ppm versus a control; however, significant decreases were observed at higher concentrations. In all except 1000 ppm mesocosms, water column Chl a increased, with a 7-fold increase at 100 ppm. These data demonstrate that at very high glyphosate concentrations, both acute toxicity and light limitation from enhanced algal biomass may have adverse impacts on seagrasses. Despite these observations, no significant adverse impacts attributed to acute toxicity were observed at 1 ppm, which is >1000 times higher than concentrations measured in the Indian River Lagoon system. Overall, herbicide use and associated decaying biomass contribute nutrients to these systems, in contrast to the removal of nutrients when mechanical harvesting is used. Based on our data and calculations, when used at recommended application rates, contributions to eutrophication, degraded water quality and harmful algal blooms were more likely to impact seagrasses than acute toxicity of glyphosate.

LC-MS metabolomics uncovers potential biomarkers of semen cryo-injury in goats.

Semen cryopreservation acts a crucial role in enhancing breed improvement and conserving genetic resources. However, it often leads to decreased sperm activity and reduced pregnancy rates. Despite significant advancements in semen freezing techniques for goats, the precise factors and mechanisms causing cryo-injury remain unclear. In this study, we examined the motility characteristics of fresh semen versus frozen-thawed semen and investigated changes in the metabolite profiles of seminal plasma using liquid chromatograph-mass spectrometry (LC-MS). A total of 364 differentially expressed metabolites (DEMs) were identified between fresh and frozen-thawed semen samples. Among these, 185 metabolites were significantly up-regulated, while 179 were down-regulated (p<0.05). The majority of these DEMs belonged to lipids and lipid-like molecules, as well as organic acids and derivatives. The Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that these DEMs were primarily involved in pathways related to amino acid synthesis and metabolism. Additionally, metabolite set enrichment analysis (MSEA) underscored the critical role of amino acid synthesis and metabolic pathways in semen cryopreservation. Specific metabolites such as alanine, proline, phenylalanine, tryptophan, tyrosine, adenosine, citric acid, flavin adenine dinucleotide (FAD), and choline emerged as potential biomarkers for sperm cryo-injury in goats. These findings provide valuable insights into enhancing the quality of semen cryopreservation in goats, contributing to improved breeding and genetic resource conservation efforts.

IL-33 Induces a Switch in Intestinal Metabolites Revealing the Tryptophan Pathway as a Target for Inducing Allograft Survival.

IL-33, a pleiotropic cytokine, has been associated with a plethora of immune-related processes, both inflammatory and anti-inflammatory. T regulatory (Treg) cells, the main leukocyte population involved in immune tolerance, can be induced by the administration of IL-33, the local microbiota, and its metabolites. Here, we demonstrate that IL-33 drastically induces the production of intestinal metabolites involved on tryptophan (Trp) metabolism. naïve mice were treated with IL-33 for 4 days and leukocyte populations were analyzed by flow cytometry, and feces were processed for microbiota and intestinal metabolites studies. Using a murine skin transplantation model, the effect of Kynurenic acid (KA) on allograft survival was tested. Under homeostatic conditions, animals treated with IL-33 showed an increment in Treg cell frequencies. Intestinal bacterial abundance analysis indicates that IL-33 provokes dysbiosis, demonstrated by a reduction in Enterobacteria and an increment in Lactobacillus genera. Furthermore, metabolomics analysis showed a dramatic IL-33 effect on the abundance of intestinal metabolites related to amino acid synthesis pathways, highlighting molecules linked to Trp metabolism, such as kynurenic acid (KA), 5-Hydroxyindoleacetic acid (5-HIAA), and 6-Hydroxynicotinic acid (6-HNA), which was supported by an enhanced expression of Ido and Kat mRNA in MLN cells, which are two enzymes involved on KA synthesis. Interestingly, animals receiving KA in drinking water and subjected to skin transplantation showed allograft acceptance, which is associated with an increment in Treg cell frequencies. Our study reveals a new property for IL-33 as a modulator of the intestinal microbiota and metabolites, especially those involved with Trp metabolism. In addition, we demonstrate that KA favors Tregs in vivo, positively affecting skin transplantation survival.

Abstract C087: Distinct gene expression and DNA methylation pattern associated with poor outcome of B-cell acute lymphoblastic leukemia in Hispanic/Latino children

Abstract The risk of developing Acute Lymphoblastic Leukemia (B-ALL) in Hispanic/Latino (HL) children is 1.2-1.75 greater that Non-Hispanic whites (NHW) and after correcting for socioeconomic factors, mortality is 40% higher in HL children. H/L children have a higher incidence of high-risk genetic variations: a 2-fold greater rate of IKZF1 deletion (IKZF1-del) and a 4-fold greater rate of CRLF2 translocations. IKZF1-del is associated with chemotherapy resistance and CRLF2 translocations represent Ph-like status. These two genetic alterations are concomitant in H/L children. 94% of H/L patients with CRLF2 translocation had a coexisting IKZF1-del. Despite evidence of specific genomic alterations in B-ALL in H/L children, potential differences in gene expression in B-ALL from H/L vs. NHW children has not been studied. Here, we used transcriptomic and genomic approach to determine the role of specific mutations and genetic background in regulation of gene expression in B-ALL from H/L and NHW children and to gain insight into molecular mechanisms that regulate cellular proliferation and chemotherapy resistance. RNA-seq was performed on B-ALL from 42 H/L and 18 NHW children and differential gene expression patterns were compared between the two ethnic groups. Gene set enrichment analysis (GSEA), Gene ontology (GO), and Ingenuity pathway analysis (IPA) were performed. In addition, we performed separate analysis and compared both ethnic groups with wild-type status of IKZF1 (IKZF1-WT). We performed DNA methylation signature analysis using reduced representation bisulfite sequencing on 8 H/L and 8 NHW B-ALL samples. Results showed increased expression of the genes that regulate Immune and inflammatory response, interferon signaling, and JAK/STAT pathway in H/L compared to NHW B-ALL cells. These expression changes were more pronounced in IKZF1-del B-All cells. In contrast, H/L B-ALL cells have reduced expression of the genes that regulate genome stability, cell cycle checkpoint signaling, and specific amino acid synthesis pathways. IPA showed upregulated interferon, Tec Kinase, and CDK5 signaling in B-ALL cells of H/L compared to NHW children. Compared. DNA Methylation analysis showed distinct patterns associated with altered expression of several oncogenes in B-ALL from H/L, compared to NHW children. In conclusion, H/L B-ALL has a distinct expression of the genes that regulate signaling pathways that promote cellular proliferation and chemotherapy resistance that are different from B-ALL in NHW children. Results identified therapeutic targets and tumor vulnerabilities that can be used for precision medicine approach to reduce disparities in B-ALL outcome in H/L children. Citation Format: Sinisa Dovat, Joseph Schramm, Daniel Bogush, Dhimant Desai, Bing He, Dhimant Desai, Arati Sharma. Distinct gene expression and DNA methylation pattern associated with poor outcome of B-cell acute lymphoblastic leukemia in Hispanic/Latino children [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C087.

Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils

Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.

The prebiotic effects of fructooligosaccharides enhance thegrowth characteristics of Staphylococcus epidermidis and enhance the inhibition of Staphylococcus aureus biofilm formation.

Oligosaccharides have been shown to enhance the production of short chain fatty acids (SCFAs) by gut probiotics and regulate gut microbiota, to improve intestinal health. Recent research indicates that oligosaccharides may also positively impact skin microbiota by selectively promoting the growth of skin commensal bacteria and inhibiting pathogenic bacteria. However, the specific metabolic and regulatory mechanisms of skin commensal bacteria in response to oligosaccharides remain unclear. This study aims to explore the influence of four oligosaccharides on the growth and metabolism of Staphylococcus epidermidis and further identify skin prebiotics that can enhance its probiotic effects on the skin. Fructooligosaccharides (FOS), isomaltooligosaccharide (IMO), galactooligosaccharides (GOS) and inulin were compared in terms of their impact on cell proliferation, SCFAs production of S. epidermidis CCSM0287 and the biofilm inhibition effect of their fermentation supernatants on Staphylococcus aureus CCSM0424. Furthermore, the effect of FOS on S. epidermidis CCSM0287 was analysed by the transcriptome analysis. All four oligosaccharides effectively promoted the growth of S. epidermidis CCSM0287 cells, increased the production of SCFAs, with FOS demonstrating the most significant effect. Analysis of the SCFAs indicated that S. epidermidis CCSM0287 predominantly employs oligosaccharides to produce acetic acid and isovaleric acid, differing from the SCFAs produced by gut microbiota. Among the four oligosaccharides, the addition of 2% FOS fermentation supernatant significantly inhibited S. aureus CCSM0424 biofilm formation. Furthermore, RNA sequencing revealed 162 differentially expressed genes (84 upregulated and 78 downregulated) of S. epidermidis CCSM0287 upon FOS treatment compared with glucose treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis highlighted differences in the amino acid synthesis pathway, particularly in terms of arginine biosynthesis. FOS promotes cell proliferation, increases the SCFA production of S. epidermidis CCSM0287 and enhance the inhibition of S. aureus biofilm formation, suggesting that FOS serves as a potential prebiotic for strain S. epidermidis CCSM0287.

Abnormal amino acid synthesis and glutathione metabolism may affect PCOS blastocyst development: an examination of in vitro mouse blastocysts model utilizing RNA-sequencing

BackgroundExtensive research has been conducted on embryonic developmental disorders linked to Polycystic Ovary Syndrome (PCOS), a pathological condition that affects 5−10% of women and is characterized by irregularities in the menstrual cycle and infertility. By employing RNA sequencing (RNA-seq), we performed an in-depth investigation of PCOS-related changes in gene expression patterns at the mouse blastocyst stage.MethodsThe zygotes of female B6D2 mice were obtained and then differentiated into blastocysts in K + Simplex Optimised Medium (KSOM) cultures containing exo-NC (negative control for exosomes) or exo-LIPE-AS1 (a novel exosomal marker of PCOS). Subsequently, blastocysts were collected for RNA-seq. The bioinformatics was performed to analyze and compare the differences of gene expression profile between blastocysts of control and PCOS group.ResultsThere were 1150 differentially expressed genes (DEGs) between the two groups of mouse blastocysts; 243 genes were upregulated and 907 downregulated in the blastocysts of the exo-LIPE-AS1 group compared to those of the exo-NC group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the genes involved in amino acid synthesis and glutathione metabolic pathways were down-regulated in exo-LIPE-AS1 group.ConclusionThis study has revealed that blastocyst developmental retardation may be associated with the downregulation of amino acid synthesis and glutathione metabolism, which may affect energy metabolism, biosynthesis, cellular osmotic pressure, antioxidant synthesis, ROS clearance or mitochondrial function, and ultimately cause blastocyst cell development abnormalities. Our research offers encouraging data on the mechanisms underlying aberrant embryonic development in patients with PCOS as well as potential treatment strategies.

The metabolic pathways of carbon assimilation and polyhydroxyalkanoate production by Rhodospirillum rubrum in response to different atmospheric fermentation.

The purple nonsulfur bacteria, Rhodospirillum rubrum, is recognized as a potential strain for PHAs bioindustrial processes since they can assimilate a broad range of carbon sources, such as syngas, to allow reduction of the production costs. In this study, we comparatively analyzed the biomass and PHA formation behaviors of R. rubrum under 100% CO and 50% CO gas atmosphere and found that pure CO promoted the PHA synthesis (PHA content up to 23.3% of the CDW). Hydrogen addition facilitated the uptake and utilization rates of CO and elevated 3-HV monomers content (molar proportion of 3-HV up to 9.2% in the presence of 50% H2). To elucidate the genetic events culminating in the CO assimilation process, we performed whole transcriptome analysis of R. rubrum grown under 100% CO or 50% CO using RNA sequencing. Transcriptomic analysis indicated different CO2 assimilation strategy was triggered by the presence of H2, where the CBB played a minor role. An increase in BCAA biosynthesis related gene abundance was observed under 50% CO condition. Furthermore, we detected the α-ketoglutarate (αKG) synthase, converting fumarate to αKG linked to the αKG-derived amino acids synthesis, and series of threonine-dependent isoleucine synthesis enzymes were significantly induced. Collectively, our results suggested that those amino acid synthesis pathways represented a key way for carbon assimilation and redox potential maintenance by R. rubrum growth under syngas condition, which could partly replace the PHA production and affect its monomer composition in copolymers. Finally, a fed-batch fermentation of the R. rubrum in a 3-l bioreactor was carried out and proved H2 addition indeed increased the PHA accumulation rate, yielding 20% ww-1 PHA production within six days.

Cloning, Expression, Enzymatic Characterization and Mechanistic Studies of M13 Mutant Acetohydroxyacid Synthase That Rescues Valine Feedback Inhibition

Acetohydroxyacid synthase (AHAS) is a key enzyme in the first step of the branched-chain amino acid synthesis pathway, and the production of acetohydroxybutyrate from one molecule of 2-ketobutyric acid and one molecule of pyruvate. AHAS is inhibited by feedback from L-valine, L-leucine, and L-isoleucine, and the expression of ilvBN, the gene encoding AHAS, is regulated by all three branched-chain amino acids. A change in amino acids 20–22 on the regulatory subunit (M13 mutation) removes the feedback inhibition by valine. We cloned the gene encoding AHAS (ilvBN) into a vector and then transfected it into Escherichia coli BL21 for expression with targeted changes in amino acids 20–22 on the regulatory subunit, and then determined the activity of the mutated AHAS and its inhibitory effects on valine, isoleucine, and leucine. The enzyme containing the M13 mutation was feedback resistant to all three amino acids. Previous studies have suggested that the binding sites for the three branched-chain amino acids may be at the same variable center. We investigated the enzymatic properties of wild-type and mutant AHAS, modeled their crystal structures, and resolved the mechanism of feedback inhibition induced by mutant M13, which will be useful for continuing the modification of AHAS and the design of broad-spectrum herbicides.

Mechanism underlying effects of cellulose-degrading microbial inoculation on amino acid degradation and biosynthesis during composting

Amino acids are essential organic compounds in composting products. However, the mechanism underlying the amino acid metabolism during composting remains unclear. This study aims at exploring the impacts of inoculating cellulose-degrading microbes on amino acid metabolism during composting with mulberry branches and silkworm excrements. Cellulose-degrading microbial inoculation enhanced amino acid degradation by 18%–43% by increasing protease and sucrase activities and stimulating eight amino acid degradation pathways from the initial to thermophilic phases, with Enterococcus, Saccharomonospora, Corynebacterium being the dominant bacterial genera, but stimulated amino acid production by 54% by increasing sucrase and urease activities, decreasing β-glucosidase activities, and stimulating twenty-two amino acid synthesis pathways at the mature phase, with Thermobifida, Devosia, and Cellulosimicrobium being the dominant bacterial genera. The results suggest that cellulose-degrading microbial inoculation enhances amino acid degradation from the initial to thermophilic phases and biosynthesis at the mature phase, thereby improving the quality of organic fertilizer.

Integrative proteomic-metabolomics strategy reveals the regulators and mechanism of enhancing cyclic lipopeptides in the high-cell-density fermentation of Bacillus subtilis S1702

The cyclic lipopeptides (CPs) are synthesized by Bacillus spp. with excellent surface activities, but are limited in the application due to its low yield. More CPs secretion was previously determined in Bacillus subtilis culture under high cell density fermentation (HF). To explore the regulators and mechanism of sporulation and CPs, the proteomic and metabolomics profiles were firstly analyzed. As results, 95 different-regulated proteins were concentrated in TCA cycle, amino acid and fatty acid synthesis and metabolism pathways, promoting the synthesis of precursor peptide chains, inducing fatty acid transformation, and indirectly enhancing the formation of the CPs. Moreover, the correlation proteomic-metabolomics analysis showed that the surfactin and iturin yield were promoted by upregulation of NRPS synthetase (Sfp, Ste), while the downregulation of FenB (log2FC=-2.35) restricted the synthesis of fengycin. Besides, the addition of KH2PO4 increased the expression of two-component system (PhoR/PhoP), and promoted sporulation indirectly. Furthermore, sufficient substrate in HF system promoted energy metabolism pathway to produce more ATP and maintain cell vitality. Overall, our findings firstly provide a basis for further exploring potential regulation of CPs secretion induced by HF, and could be as a novel guild for look for the regulator of target substance in fermentation.

Restricted glycolysis is a primary cause of the reduced growth rate of zinc-deficient yeast cells

Zinc is required for many critical processes, including intermediary metabolism. In Saccharomyces cerevisiae, the Zap1 activator regulates the transcription of ∼80 genes in response to Zn supply. Some Zap1-regulated genes are Zn transporters that maintain Zn homeostasis, while others mediate adaptive responses that enhance fitness. One adaptive response gene encodes the 2-cysteine peroxiredoxin Tsa1, which is critical to Zn-deficient (ZnD) growth. Depending on its redox state, Tsa1 can function as a peroxidase, a protein chaperone, or a regulatory redox sensor. In a screen for possible Tsa1 regulatory targets, we identified a mutation (cdc19S492A) that partially suppressed the tsa1Δ growth defect. The cdc19S492A mutation reduced activity of its protein product, pyruvate kinase isozyme 1 (Pyk1), implicating Tsa1 in adapting glycolysis to ZnD conditions. Glycolysis requires activity of the Zn-dependent enzyme fructose-bisphosphate aldolase 1, which was substantially decreased in ZnD cells. We hypothesized that in ZnD tsa1Δ cells, the loss of a compensatory Tsa1 regulatory function causes depletion of glycolytic intermediates and restricts dependent amino acid synthesis pathways, and that the decreased activity of Pyk1S492A counteracted this depletion by slowing the irreversible conversion of phosphoenolpyruvate to pyruvate. In support of this model, supplementing ZnD tsa1Δ cells with aromatic amino acids improved their growth. Phosphoenolpyruvate supplementation, in contrast, had a much greater effect on growth rate of WT and tsa1Δ ZnD cells, indicating that inefficient glycolysis is a major factor limiting yeast growth. Surprisingly however, this restriction was not primarily due to low fructose-bisphosphate aldolase 1 activity, but instead occurs earlier in glycolysis.

Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration.

Previous studies have revealed tight metabolic complementarity between bivalves and their endosymbiotic chemosynthetic bacteria, but little is known about their interactions with ectosymbionts. Our analysis of the ectosymbiosis between a deep-sea scallop (Catillopecten margaritatus) and a gammaproteobacterium showed that bivalves could be highly interdependent with their ectosymbionts as well. Our microscopic observation revealed abundant sulfur-oxidizing bacteria (SOB) on the surfaces of the gill epithelial cells. Microbial 16S rRNA gene amplicon sequencing of the gill tissues showed the dominance of the SOB. An analysis of the SOB genome showed that it is substantially smaller than its free-living relatives and has lost cellular components required for free-living. Genomic and transcriptomic analyses showed that this ectosymbiont relies on rhodanese-like proteins and SOX multienzyme complex for energy generation, mainly on the Calvin-Benson-Bassham (CBB) cycle and peripherally on a phosphoenolpyruvate carboxylase for carbon assimilation. Besides, the symbiont encodes an incomplete tricarboxylic acid (TCA) cycle. Observation of the scallop's digestive gland and its nitrogen metabolism pathways indicates it does not fully rely on the ectosymbiont for nutrition. Analysis of the host's gene expression provided evidence that it could offer intermediates for the ectosymbiont to complete its TCA cycle and some amino acid synthesis pathways using exosomes, and its phagosomes, endosomes, and lysosomes might be involved in harvesting nutrients from the symbionts. Overall, our study prompts us to rethink the intimacy between the hosts and ectosymbionts in Bivalvia and the evolution of chemosymbiosis in general.

Engineering allosteric inhibition of homoserine dehydrogenase by semi-rational saturation mutagenesis screening.

Allosteric regulation by pathway products plays a vital role in amino acid metabolism. Homoserine dehydrogenase (HSD), the key enzyme for the biosynthesis of various aspartate family amino acids, is subject to feedback inhibition by l-threonine and l-isoleucine. The desensitized mutants with the potential for amino acid production remain limited. Herein, a semi-rational approach was proposed to relieve the feedback inhibition. HSD from Corynebacterium glutamicum (CgHSD) was first characterized as a homotetramer, and nine conservative sites at the tetramer interface were selected for saturation mutagenesis by structural simulations and sequence analysis. Then, we established a high-throughput screening (HTS) method based on resistance to l-threonine analog and successfully acquired two dominant mutants (I397V and A384D). Compared with the best-ever reported desensitized mutant G378E, both new mutants qualified the engineered strains with higher production of CgHSD-dependent amino acids. The mutant and wild-type enzymes were purified and assessed in the presence or absence of inhibitors. Both purified mutants maintained >90% activity with 10mMl-threonine or 25mMl-isoleucine. Moreover, they showed >50% higher specific activities than G378E without inhibitors. This work provides two competitive alternatives for constructing cell factories of CgHSD-related amino acids and derivatives. Moreover, the proposed approach can be applied to engineering other allosteric enzymes in the amino acid synthesis pathway.

Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome.

The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages. In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes. The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways. This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.

High-throughput sequencing analysis of the characteristics of the gut microbiota in aged patients with sarcopenia

BackgroundThe gut microbiota is a complex microbial community that changes in response to various intestinal diseases, including aging-related diseases such as sarcopenia. Several studies have shown that the metabolites of the gut microbiota affect the dynamic balance of the skeletal muscle. However, the effect of gut microbiota imbalance on sarcopenia is still largely unknown. MethodsWe collected the baseline characteristics and fecal samples of 14 patients with sarcopenia and 21 patients without sarcopenia, and used the 16S rRNA sequencing technology to analyze the differences in the gut microbiota in the two groups. α-diversity and β-diversity were employed to assess the abundance and diversity of species and variations in microflora composition, respectively. Moreover, Tax4Fun was employed to predict the functional capacities of the microbial communities. ResultsIn the sarcopenia group, the abundances of beneficial bacteria such as Bacteroides, Faecalibacterium, Fusobacterium, and Prevotella were reduced, whereas those of pathogenic bacteria, such as Escherichia-Shigella and Klebsiella, were increased. The genera and species of the family Enterobacteriaceae were the main pathogenic bacteria in patients with sarcopenia, and Escherichia-Shigella and Klebsiella could be used as key biomarkers of sarcopenia. The defective protein processing and amino acid synthesis pathways in patients with sarcopenia indicated that protein synthesis and nutrient transport may be damaged. Moreover, the abundances of Escherichia-Shigella and Enterobacteriaceae have been found to have a negative correlation with muscle mass and were the main parameters predicting the change in muscle mass. ConclusionsIn this study, we have identified changes in the gut microbiota of sarcopenic individuals, which were linked to the loss of muscle mass and function. Escherichia-Shigella is a conditional pathogen of sarcopenic patients, and its levels are found to have a significant negative correlation with muscle mass.

Widely targeted metabolomic analysis reveals that volatile metabolites in cigar tobacco leaves dynamically change during fermentation

Changes in volatile metabolites during cigar tobacco leaves fermentation as well as the metabolic pathways of metabolites with significant differences were investigated to determine the influence of cigar tobacco leaves fermentation on its flavor. The volatile substances in cigar tobacco leaves at different stages were detected by headspace-solid phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS), and the main differences in volatile substances in cigar tobacco leaves at different fermentation stages of Yunxue1 in Yuxi production area were analyzed by principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA). The results show that in the process of cigar tobacco leaves fermentation (YXF0, YXF1, YXF2, YXF3, YXF4, YXF5), a total of 613 volatile metabolites were detected, and a significant difference was found in 263 kinds of metabolites. Among them, the main upregulated differential metabolites were 1,3,6,10-Cyclotetradecatetraene, 3,7,11-trimethyl-14-(1-methylethyl)-, [S-(E,Z,E,E)]-, Benzoic acid, Benzaldehyde, etc. While the main downregulated differential metabolites included beta.-Myrcene, trans-Farnesol, etc. The metabolites with significant differences are mainly concentrated in the biosynthesis of monoterpenes, diterpenes, sesquiterpenes and triterpenes, the degradation metabolism of amino acids, such as valine, leucine and isoleucine, and the biosynthesis of phenylpropyl. There were 8 different metabolites in 5 groups, including 4- (1-methylethyl) -1-cyclohexene-1-formaldehyde、2, 4-dihydroxyacetophenone、2-methylbutyl 3-methylbutyrate and methylpyrazine, all of which showed upregulation trend during fermentation. In the fermentation process, volatile metabolites participate in various synthesis and degradation pathways. The biosynthesis pathway of terpenes and amino acid synthesis and degradation pathway are connected to produce various terpenes, aldehydes and other substances, such as 1,3,6,10-Cyclotetradecatetraene, 3,7,11-trimethyl-14-(1-methylethyl)-, [S-(E,Z,E,E)]-、benzaldehyde and 4-hydroxybenzaldehyde, which are conducive to the overall flavor and quality of cigar tobacco leaves.

Traditional, Mixed-Mode, and Online Instruction for Microbial Metabolism Before and During COVID-19

As COVID-19 restrictions are removed, instructors are faced with two questions: should the course be taught online, via mixed-mode, or through traditional methods, and what effect did online instruction have on students in the course in regards regarding enrolled across eight semesters of metabolism courses using traditional, mixed-mode, and online methods. Post-hoc analysis of a repeated-measures ANOVA determined that while mixed-mode outperformed traditional methods on metabolism exams involving introductory concepts on the first exam (4.47 ±4.24, p= 0.012) and on the cumulative final exam (8.15 ±4.24, p= &lt;0.001), traditional methods were superior to both mixed-mode (9.21 ±4.24, p= &lt;0.001) and online methods (6.37 ±5.76, p= 0.006) at teaching alternative pathways of metabolism and lipid, nucleotide, and amino acid synthesis pathways. All methods showed poor student scores on glycolysis, TCA cycle, oxidative phosphorylation topics. Online methods performed nearly equally to mixed-mode, though there was not a significant difference on the first exam’s content as was found with mixed-mode. It is evident that, based on this study, a different approach to teaching basic central metabolic cycles such as glycolysis, the TCA cycle, and the electron transport chain is necessary to improve student understanding of these topics.

Microbiome analysis reveals potential for modulation of gut microbiota through polysaccharide-based prebiotic feeding in Oreochromis niloticus (Linnaeus, 1758).

Characterization and functional profiling of the gut microbiota are essential for guiding nutritional interventions in fish and achieving favorable host-microbe interactions. Thus, we conducted a 30days study to explore and document the gut microbial community of O. niloticus, as well as to evaluate the effects of a polysaccharide-based prebiotics with 0.5% and 0.75% Aloe vera extract on the gut microbiome through genomic analysis. The V3-V4 region of 16S rRNA was amplified and sequenced using Illumina HiSeq 2500, resulting in 1,000,199 reads for operational taxonomic unit (OTU) identification. Out of 8,894 OTUs, 1,181 were selected for further analysis. Our results revealed that Planctomycetes, Firmicutes, Proteobacteria, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in both control and treatment samples. Higher doses of prebiotics were found to improve Planctomycetes and Firmicutes while decreasing Proteobacteria and Verrucomicrobia. We observed increasing trends in the abundance of Bacilli, Bacillaceae, and Bacillus bacteria at the class, family, and genus levels, respectively, in a dose-dependent manner. These findings were consistent with the conventional colony count data, which showed a higher prevalence of Bacillus in prebiotic-supplemented groups. Moreover, predicted functional analysis using PICRUSt indicated a dose-dependent upregulation in glycolysis V, superpathway of glycol metabolism and degradation, glucose and xylose degradation, glycolysis II, and sulfoglycolysis pathways. Most of the energy, protein, and amino acid synthesis pathways were upregulated only at lower doses of prebiotic treatment. Our findings suggest that the gut microbiome of O. niloticus can be optimized through nutritional interventions with plant-based polysaccharides for improved growth performance in commercial fish.

Integrative analysis of exogenous auxin mediated plant height regulation in Moso bamboo (Phyllostachys edulis)

Auxin is important in regulating bamboo growth and development. Morphological and anatomical analyses of naturally growing Moso bamboo treated with auxin revealed that auxin-mediated regulation of bamboo height mainly increased internode length rather than nodes number. For individual internodes, auxin regulated internode elongation mainly by promoting cell elongation. Targeted metabolomic assays of endogenous hormones found that exogenous auxin treatment affected the dynamic balance of endogenous hormones, resulting in increased levels of gibberellin and cytokinin. Transcriptome sequencing indicated that the regulation of internode length by auxin is mainly through phytohormone signaling pathway, amino acid synthesis and protein processing pathway, and energy metabolism pathway. The transcription factors that play major regulatory roles included the ethylene response factor, WRKY and MYB transcription factor, NAC structural domain protein and basic leucine zipper protein. By constructing a gene regulatory network, we found that auxin may crosstalk with multiple plant hormones. Yeast two-hybrid and transgenic experiments demonstrated that the auxin signaling factor PheAUX/IAA34 and the jasmonic acid signaling factor PheTIFY28 do interact and regulate growth in response to phytohormones. Overall we have obtained good quality bamboo internode material for industry through the auxin treatment and have preliminarily investigated the mechanism, which will provide a reference for bamboo plant height regulation.