Amino Acid Biosynthesis Pathways Research Articles

Transcriptome Analysis and Validation of Anthracnose Resistance Genes in Walnut Varieties

Anthracnose is extremely detrimental to walnut production, because it seriously affects its yield. Therefore, this study aimed to identify anthracnose resistance genes in walnuts, to lay the foundation for cultivating novel anthracnose-resistant walnut varieties. In this study, the fruits of walnut varieties “Qinyou 1” and “Qinyou 2”, exhibiting relatively weak resistance to anthracnose, were used for transcriptome sequencing and identifying differentially expressed genes (DEGs). Thereafter, we used a quantitative real-time polymerase chain reaction to verify the reliability of the transcriptome data using the walnut varieties Qinyou 1, Qinyou 2, Qinyou 3, Liaohe 1, and Diamond 1. We identified 6326 DEGs post-infection in Qinyou 1, of which 3065 were upregulated and 3261 were downregulated. We also found 2055 DEGs (969 upregulated and 1086 downregulated genes) in the two varieties, after 6 days of anthracnose infection. Based on GO and KEGG enrichment analyses of the transcriptome data, we noted that the DEGs were primarily involved in metabolic processes, cell composition, cell structure, catalytic activity, and binding activity. Furthermore, KEGG functional enrichment analysis showed that the amino acid biosynthesis pathway and plant–pathogen interaction may be activated under anthracnose infection. We also noted that the expression levels of anthracnose resistance genes in different walnut varieties were significantly different. Thus, the findings of this study provide important genetic resources and molecular markers for the cultivation of novel anthracnose-resistant walnut varieties.

Integrated transcriptomic and metabolomic data reveal the cold stress responses molecular mechanisms of two coconut varieties.

Among tropical fruit trees, coconut holds significant edible and economic importance. The natural growth of coconuts faces a challenge in the form of low temperatures, which is a crucial factor among adverse environmental stresses impacting their geographical distribution. Hence, it is essential to enhance our comprehension of the molecular mechanisms through which cold stress influences various coconut varieties. We employed analyses of leaf growth morphology and physiological traits to examine how coconuts respond to low temperatures over 2-hour, 8-hour, 2-day, and 7-day intervals. Additionally, we performed transcriptome and metabolome analyses to identify the molecular and physiological shifts in two coconut varieties displaying distinct sensitivities to the cold stress. As the length of cold stress extended, there was a prominent escalation within the soluble protein (SP), proline (Pro) concentrations, the activity of peroxidase (POD) and superoxide dismutase (SOD) in the leaves. Contrariwise, the activity of glutathione peroxidase (GSH) underwent a substantial reduction during this period. The widespread analysis of metabolome and transcriptome disclosed a nexus of genes and metabolites intricately cold stress were chiefly involved in pathways centered around amino acid, flavonoid, carbohydrate and lipid metabolism. We perceived several stress-responsive metabolites, such as flavonoids, carbohydrates, lipids, and amino acids, which unveiled considerably, lower in the genotype subtle to cold stress. Furthermore, we uncovered pivotal genes in the amino acid biosynthesis, antioxidant system and flavonoid biosynthesis pathway that presented down-regulation in coconut varieties sensitive to cold stress. This study broadly enriches our contemporary perception of the molecular machinery that contributes to altering levels of cold stress tolerance amid coconut genotypes. It also unlocks several unique prospects for exploration in the areas of breeding or engineering, aiming to identifying tolerant and/or sensitive coconut varieties encompassing multi-omics layers in response to cold stress conditions.

Dietary crude protein and protein solubility manipulation enhances intestinal nitrogen absorption and mitigates reactive nitrogen emissions through gut microbiota and metabolome reprogramming in sheep

Dietary nutrient manipulation (e.g. protein fractions) could lower the environmental footprints of ruminants, especially reactive nitrogen (N). This study investigated the impacts of dietary soluble protein (SP) levels with decreased crude protein (CP) on intestinal N absorption, hindgut N metabolism, fecal microbiota and metabolites, and their linkage with N metabolism phenotype. Thirty-two male Hu sheep, with an age of six months and an initial BW of 40.37 ± 1.18 kg, were randomly assigned to four dietary groups. The control diet (CON), aligning with NRC standards, maintained a CP content of 16.7% on a dry matter basis. Conversely, the experimental diets (LPA, LPB, and LPC) featured a 10% reduction in CP compared with CON, accompanied by SP adjustments to 21.2%, 25.9%, and 29.4% of CP, respectively. Our results showed that low-protein diets led to significant reductions in the concentrations of plasma creatinine, ammonia, urea N, and fecal total short-chain fatty acids (SCFA) (P < 0.05). Notably, LPB and LPC exhibited increased total SCFA and propionate concentrations compared with LPA (P < 0.05). The enrichment of the Prevotella genus in fecal microbiota associated with energy metabolism and amino acid (AA) biosynthesis pathways was evident with SP levels in low-protein diets of approximately 25% to 30%. Moreover, LPB and LPC diets demonstrated a decrease in fecal NH4+–N and NO2−–N contents as well as urease activity, compared with CON (P < 0.05). Concomitantly, reductions in fecal glutamic acid dehydrogenase gene (gdh), nitrite reductase gene (nirS), and nitric oxide reductase gene (norB) abundances were observed (P < 0.05), pointing towards a potential reduction in reactive N production at the source. Of significance, the up-regulation of mRNA abundance of AA and peptide transporters in the small intestine (duodenum, jejunum, and ileum) and the elevated concentration of plasma AA (e.g. arginine, methionine, aspartate, glutamate, etc.) underscored the enhancement of N absorption and N efficiency. In summary, a 10% reduction in CP, coupled with an SP level of approximately 25% to 30%, demonstrated the potential to curtail reactive N emissions through fecal Prevotella enrichment and improve intestinal energy and N utilization efficiency.

Synbiotic regulates gut microbiota in patients with lupus nephritis: an analysis using metagenomic and metabolome sequencing.

To investigate the changes in gut microbes and their metabolites after administering synbiotics to patients with new-onset lupus nephritis (LN) treated using a conventional method and provide a theoretical basis for finding new targets for the diagnosis and treatment of LN. In this study, a total of 12 participants were divided into the lupus and synbiotic groups. Stool samples and clinical data were collected before and after treatment for metagenomic, nontargeted metabolomic, and statistical analyses. The relative abundances of the pathogenic bacteria Prevotella, Bacteroides, and Enterobacteriaceae_unclassified decreased after synbiotic treatment, whereas the abundances of Actinobacteria and Firmicutes increased. Further, the Firmicutes to Bacteroidetes ratio increased; however, the difference was not statistically significant (p > 0.05). α diversity analysis showed no significant differences in the intestinal microbial richness and diversity index of patients with LN between the groups before and after treatment (p > 0.05). β analysis showed the differences in the community structure between the samples of the two groups before and after treatment. Linear discriminant analysis effect size and receiver operating characteristic curve analyses revealed that Negativicutes (AUC = 0.9722) and Enterobacteriaceae_unclassified (AUC = 0.9722) were the best predictors of the lupus and synbiotic groups, respectively, before and after treatment. Joint analyses revealed that amino acid biosynthesis, aminoacyl-tRNA biosynthesis, purine metabolism, and other metabolic pathways may be involved in the changes in the metabolic function of patients with LN after the addition of synbiotics. Spearman's correlation analysis revealed the interaction between clinical features and flora, and flora exhibited a complex biological network regulatory relationship. Synbiotics regulate the metabolic functions of intestinal microorganisms in patients with LN and play a role in various biological functions. Synbiotic supplements may be safe and promising candidates for patients with LN.

Integrated proteomics and metabolomics analysis reveals the molecular mechanism of PP/PBAT-modified atmosphere packaging for the preservation of Allium mongolicum Regel

Allium mongolicum Regel (A. mongolicum) is a healthy edible plant but highly perishable with a short shelf life of 1–2 d. Herein, integrated proteomics and metabolomics analyses of A. mongolicum at 0 and 18 d during storage were performed to explore the preservation mechanism of A. mongolicum. The results manifested that the polypropylene/poly (butylene adipate-co-terephthalate) (PP/PBAT, abbreviated as PAT) modified atmosphere packaging better maintained the freshness of A. mongolicum and effectively reduced the respiration rate and decay rate of A. mongolicum. A total of 4336 proteins were identified by proteomic analysis, of which 291 proteins were significantly differentially expressed. Metabolomics identified 782 metabolites, among which 65 metabolites were notably altered during storage. The differential proteins and metabolites were primarily involved in the pathways of amino acid biosynthesis, 2-oxocarboxylic acid metabolism, galactose metabolism, lipid oxidation and metabolism, and starch and sucrose metabolism, which are regulated by transcription and translation. PAT packaging inhibited proteolysis and up-regulated antioxidant-related proteins, glutathione was a key antioxidant protein that could scavenge free radicals from cells in the preservation of A. mongolicum. Meanwhile, PAT packaging with a suitable gas component favored the reduction of the tricarboxylic acid cycle, and showed down the consumption of sucrose in A. mongolicum, thereby inhibiting the respiration rate of the A. mongolicum. Furthermore, PAT packaging strengthened and maintained the cell wall structure by reducing hemicellulose degradation and lipid oxidation. Thus, PAT packaging could maintain postharvest quality of A. mongolicum. This study provides new insights into the application of modified atmosphere packaging in the preservation of A. mongolicum.

Integrative physiological, metabolomic, and transcriptomic analysis reveals the drought responses of two apple rootstock cultivars

BackgroundDrought is considered the main environmental factor restricting apple production and thus the development of the apple industry. Rootstocks play an important role in enhancing the drought tolerance of apple plants. Studies of the physiology have demonstrated that ‘ZC9-3’ is a strong drought-resistant rootstock, whereas ‘Jizhen-2’ is a weak drought-resistant rootstock. However, the metabolites in these two apple rootstock varieties that respond to drought stress have not yet been characterized, and the molecular mechanisms underlying their responses to drought stress remain unclear.ResultsIn this study, the physiological and molecular mechanisms underlying differences in the drought resistance of ‘Jizhen-2’ (drought-sensitive) and ‘ZC9-3’ (drought-resistant) apple rootstocks were explored. Under drought stress, the relative water content of the leaves was maintained at higher levels in ‘ZC9-3’ than in ‘Jizhen-2’, and the photosynthetic, antioxidant, and osmoregulatory capacities of ‘ZC9-3’ were stronger than those of ‘Jizhen-2’. Metabolome analysis revealed a total of 95 and 156 differentially accumulated metabolites in ‘Jizhen-2’ and ‘ZC9-3’ under drought stress, respectively. The up-regulated metabolites in the two cultivars were mainly amino acids and derivatives. Transcriptome analysis revealed that there were more differentially expressed genes and transcription factors in ‘ZC9-3’ than in ‘Jizhen-2’ throughout the drought treatment. Metabolomic and transcriptomic analysis revealed that amino acid biosynthesis pathways play key roles in mediating drought resistance in apple rootstocks. A total of 13 metabolites, including L-α-aminoadipate, L-homoserine, L-threonine, L-isoleucine, L-valine, L-leucine, (2S)-2-isopropylmalate, anthranilate, L-tryptophan, L-phenylalanine, L-tyrosine, L-glutamate, and L-proline, play an important role in the difference in drought resistance between ‘ZC9-3’ and ‘Jizhen-2’. In addition, 13 genes encoding O-acetylserine-(thiol)-lyase, S-adenosylmethionine synthetase, ketol-acid isomeroreductase, dihydroxyacid dehydratase, isopropylmalate isomerase, branched-chain aminotransferase, pyruvate kinase, 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase, N-acetylglutamate-5-P-reductase, and pyrroline-5-carboxylate synthetase positively regulate the response of ‘ZC9-3’ to drought stress.ConclusionsThis study enhances our understanding of the response of apple rootstocks to drought stress at the physiological, metabolic, and transcriptional levels and provides key insights that will aid the cultivation of drought-resistant apple rootstock cultivars. Especially, it identifies key metabolites and genes underlying the drought resistance of apple rootstocks.

Multi-omics analysis provides insight into the genetic basis of proline-derived milk microbiota in buffalo

Understanding the intricate relationship between genetics, metabolites, and microbiota is paramount for unraveling the complexities that define buffalo milk composition. In this study, we employed a multi-omics approach to dissect the genetic and metabolic determinants of buffalo milk traits. Metabolomics analysis of 100 buffalo milk samples revealed a rich profile of 446 metabolites, with a particular emphasis on those associated with amino acid biosynthesis. Metabolite-based Genome-Wide Association Studies (mGWAS) uncovered 13 significant genetic variants, with a pronounced focus on l-Proline. Notably, single nucleotide polymorphisms (SNPs) within the ATG16L1 gene implicated its role in proline production. Concurrently, an in-depth exploration of milk microbiota dynamics highlighted marked differences between buffaloes with high and low proline groups. High proline abundance correlated with increased microbial diversity, dominated by Firmicutes and Proteobacteria. Distinct genera, such as Acinetobacter and Corynebacterium, characterized low and high proline groups, respectively. Functional changes in milk microbiota, especially in amino acid biosynthesis pathways, underscored proline's pivotal role in shaping microbial functions. Correlations between milk microbiota abundance and proline levels emphasized the intricate relationship between host physiology and microbial composition. These findings not only advance our understanding of the genetic basis of metabolic traits in buffalo milk but also present potential biomarkers for targeted breeding strategies. This integrated approach provides a nuanced perspective on milk composition, offering implications for dairy quality and nutritional enhancement.

Binary probiotic fermentation promotes signal (cyclic AMP) exchange to increases the number of viable probiotics, anthocyanins and polyphenol content, and the odor scores of wolfberry fermented beverages

The effects and underlying molecular mechanisms of binary probiotics (Lactiplantibacillus plantarum subsp. plantarum CGMCC 1.5953 and Lacticaseibacillus casei CGMCC 1.5956) on the quality of wolfberry fermented beverages (WFB) were investigated. The results indicated that binary probiotics increased the number of probiotics, anthocyanin (89.92 ± 1.64 mg/L), polyphenol content (283.04 ± 3.81 µg/mL), and odor score (24.19) in WFB. Metabolomics found that they could enhance signal exchange (cyclic AMP) between binary probiotics and improve the utilization of citrulline, d-proline, d-glucose, and d-galactose through galactose metabolism and amino acid biosynthesis pathway to promote probiotics growth. Furthermore, HS-SPME-GC–MS and GS-IMS revealed that the improvement in flavor was mainly due to an increase in the content of the aromatic flavor substances 3-heptanol, glutaraldehyde, and 2-heptanone, and a decrease in the content of the off-flavor substances methyl isobutyl ketone-D and 2-undecanone. This is strategically important for the development of WFB with high probiotic content and unique flavor.

A higher butyrate-generation capacity of water-extractable substrates from wheat bran as evidenced by in vitro and in vivo fermentation

Gut microbiota is influenced by the dietary composition and plays important roles in the pathogenesis of metabolic disorders. Thus, wheat bran extract was prepared by either water extraction or enzymatic pre-treatment extraction (referred as AEWB and EHWB, respectively), and then their corresponding impact on short-chain fatty acids generation and gut microbiota was investigated via both in vitro fermentation model and in vivo diabetic animal model. The results of in vitro model indicated that EHWB enhanced the abundance of Megamonas and Faecalibacterium, as well as the amino acids metabolism, which was consistent with the increased butyrate and amino acids metabolites (e.g. iso-butyrate and valerate). The diabetic model analysis suggested that the rats also had an increased amino acid metabolism due to the decreased pathways of amino acid biosynthesis and increased pathways of amino acid degradation following the EHWB intervention. Importantly, the current study revealed that the EHWB intervention led to a greater level of butyrate in the diabetic animal model compared to other groups, demonstrating its prebiotic function, which was supported by the positive correlation between butyrate level and abundance of Bifidobacterium and Lactobacillus. The above results indicated that the main components in water-extractable substrates played key roles in improving the gut microbiota profile and the key metabolite in terms of butyrate. This study might highlight a new ingredient for food industry with physiological functionality.

Molecular physiology of Antarctic diatom natural assemblages and bloom event reveal insights into strategies contributing to their ecological success.

In the Southern Ocean, phytoplankton must cope with harsh environmental conditions such as low light and growth-limiting concentrations of the micronutrient iron. Using metratranscriptomics, we assessed the influence of oceanographic variables on the diversity of the phytoplankton community composition and on the metabolic strategies of diatoms along the Western Antarctic Peninsula, a region undergoing rapid climate change. We found that cross-shelf differences in oceanographic parameters such as temperature and variable nutrient concentrations account for most of the differences in phytoplankton community composition and metabolism. We opportunistically characterized the metabolic underpinnings of a large bloom of the centric diatom Actinocyclus in coastal waters of the WAP. Our results indicate that physicochemical differences from onshore to offshore are stronger than between southern and northern regions of the WAP; however, these trends could change in the future, resulting in poleward shifts in functional differences in diatom communities and phytoplankton blooms.

Integrated metabolomics and transcriptomics analysis highlight key pathways involved in the somatic embryogenesis of Darjeeling tea.

Darjeeling tea is a globally renowned beverage, which faces numerous obstacles in sexual reproduction, such as self-incompatibility, poor seed germination, and viability, as well as issues with vegetative propagation. Somatic embryogenesis (SE) is a valuable method for rapid clonal propagation of Darjeeling tea. However, the metabolic regulatory mechanisms underlying SE in Darjeeling tea remain largely unknown. To address this, we conducted an integrated metabolomics and transcriptomics analysis of embryogenic callus (EC), globular embryo (GE), and heart-shaped embryo (HE). The integrated analyses showed that various genes and metabolites involved in the phenylpropanoid pathway, auxin biosynthesis pathway, gibberellin, brassinosteroid and amino acids biosynthesis pathways were differentially enriched in EC, GE, and HE. Our results revealed that despite highly up-regulated auxin biosynthesis genes YUC1, TAR1 and AAO1 in EC, endogenous indole-3-acetic acid (IAA) was significantly lower in EC than GE and HE. However, bioactive Gibberellin A4 displayed higher accumulation in EC. We also found higher BABY BOOM (BBM) and Leafy cotyledon1 (LEC1) gene expression in GE along with high accumulation of castasterone, a brassinosteroid. Total flavonoids and phenolics levels were elevated in GE and HE compared to EC, especially the phenolic compound chlorogenic acid was highly accumulated in GE. Integrated metabolome and transcriptome analysis revealed enriched metabolic pathways, including auxin biosynthesis and signal transduction, brassinosteroid, gibberellin, phenylpropanoid biosynthesis, amino acids metabolism, and transcription factors (TFs) during SE in Darjeeling tea. Notably, EC displayed lower endogenous IAA levels, conducive to maintaining differentiation, while higher IAA concentration in GE and HE was crucial for preserving embryo identity. Additionally, a negative correlation between bioactive gibberellin A4 (GA4) and IAA was observed, impacting callus growth in EC. The high accumulation of chlorogenic acid, a phenolic compound, might contribute to the low success rate in GE and HE formation in Darjeeling tea. TFs such as BBM1, LEC1, FUS3, LEA, WOX3, and WOX11 appeared to regulate gene expression, influencing SE in Darjeeling tea.

In silico prediction of candidate gene targets for the management of African cassava whitefly (Bemisia tabaci, SSA1-SG1), a key vector of viruses causing cassava brown streak disease.

Whiteflies (Bemisia tabaci sensu lato) have a wide host range and are globally important agricultural pests. In Sub-Saharan Africa, they vector viruses that cause two ongoing disease epidemics: cassava brown streak disease and cassava mosaic virus disease. These two diseases threaten food security for more than 800 million people in Sub-Saharan Africa. Efforts are ongoing to identify target genes for the development of novel management options against the whitefly populations that vector these devastating viral diseases affecting cassava production in Sub-Saharan Africa. This study aimed to identify genes that mediate osmoregulation and symbiosis functions within cassava whitefly gut and bacteriocytes and evaluate their potential as key gene targets for novel whitefly control strategies. The gene expression profiles of dissected guts, bacteriocytes and whole bodies were compared by RNAseq analysis to identify genes with significantly enriched expression in the gut and bacteriocytes. Phylogenetic analyses identified three candidate osmoregulation gene targets: two α-glucosidases, SUC 1 and SUC 2 with predicted function in sugar transformations that reduce osmotic pressure in the gut; and a water-specific aquaporin (AQP1) mediating water cycling from the distal to the proximal end of the gut. Expression of the genes in the gut was enriched 23.67-, 26.54- and 22.30-fold, respectively. Genome-wide metabolic reconstruction coupled with constraint-based modeling revealed four genes (argH, lysA, BCAT & dapB) within the bacteriocytes as potential targets for the management of cassava whiteflies. These genes were selected based on their role and essentiality within the different essential amino acid biosynthesis pathways. A demonstration of candidate osmoregulation and symbiosis gene targets in other species of the Bemisia tabaci species complex that are orthologs of the empirically validated osmoregulation genes highlights the latter as promising gene targets for the control of cassava whitefly pests by in planta RNA interference.

Differential analysis of IBV-infected primary chicken embryonic fibroblasts and immortalized DF-1.

Infectious bronchitis virus (IBV) is responsible for high morbidity and mortality as well as substantial economic losses worldwide. Transcriptome sequencing of IBV-infected chicken embryonic fibroblast and DF-1 cells revealed that the virus elicits antiviral immunity in cells after viral infection, but IBV cannot activate DF-1 cells to produce sufficient amounts of viral structures to assemble into complete virions, which may be caused by the interactions between cytokines. The study of IBV cellular adaptations is important for vaccine development and investigation of the pathogenesis of IBV.

Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift

ABSTRACT The majority of cohort-specific studies associating gut microbiota with obesity are often contradictory; thus, the replicability of the signature remains questionable. Moreover, the species that drive obesity-associated functional shifts and their replicability remain unexplored. Thus, we aimed to address these questions by analyzing gut microbial metagenome sequencing data to develop an in-depth understanding of obese host-gut microbiota interactions using 3329 samples (Obese, n = 1494; Control, n = 1835) from 17 different countries, including both 16S rRNA gene and metagenomic sequence data. Fecal metagenomic data from diverse geographical locations were curated, profiled, and pooled using a machine learning-based approach to identify robust global signatures of obesity. Furthermore, gut microbial species and pathways were systematically integrated through the genomic content of the species to identify contributors to obesity-associated functional shifts. The community structure of the obese gut microbiome was evaluated, and a reproducible depletion of diversity was observed in the obese compared to the lean gut. From this, we infer that the loss of diversity in the obese gut is responsible for perturbations in the healthy microbial functional repertoire. We identified 25 highly predictive species and 37 pathway associations as signatures of obesity, which were validated with remarkably high accuracy (AUC, Species: 0.85, and pathway: 0.80) with an independent validation dataset. We observed a reduction in short-chain fatty acid (SCFA) producers (several Alistipes species, Odoribacter splanchnicus, etc.) and depletion of promoters of gut barrier integrity (Akkermansia muciniphila and Bifidobacterium longum) in obese guts. Our analysis underlines SCFAs and purine/pyrimidine biosynthesis, carbohydrate metabolism pathways in control individuals, and amino acid, enzyme cofactor, and peptidoglycan biosynthesis pathway enrichment in obese individuals. We also mapped the contributors to important obesity-associated functional shifts and observed that these are both dataset-specific and shared across the datasets. In summary, a comprehensive analysis of diverse datasets unveils species specifically contributing to functional shifts and consistent gut microbial patterns associated to obesity.

Chlamydiae in corals: shared functional potential despite broad taxonomic diversity.

Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.

Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen.

Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1μl of 100nmol/l amino acids comparable to a mere 1 [Formula: see text] 104-105 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the occurrence of both the Wood-Ljungdahl pathway and an incomplete reductive tricarboxylic acid cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acids, genomic information, and public databases. Among them, the presence of alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS can be considered the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to any kind of isolated microbe.

Investigating the regulatory effect of Shen Qi Bu Qi powder on the gastrointestinal flora and serum metabolites in calves.

To investigate the effects of Shen Qi Bu Qi Powder (SQBQP) on the average daily gain, blood indexes, gastrointestinal microflora, and serum metabolites of calves. A total of 105 calves were randomly assigned to three groups (n = 35 per group): the control group (C, fed with a basal diet for 21 days) and two treatment groups (SQBQP-L and SQBQP-H, fed with the basal diet supplemented with 15 and 30 g/kg of SQBQP), respectively for 21 days. The active components of SQBQP were identified using LC-MS/MS. Serum digestive enzymes and antioxidant indices were determined by ELISA kits and biochemical kits, respectively. Serum differential metabolites were analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), while flora in rumen fluid and fecal were analyzed by 16S rDNA sequencing. Further correlation analysis of gastrointestinal flora and serum metabolites of SQBQP-H and C groups were performed with Spearman's correlation. The principal active components of SQBQP mainly includes polysaccharides, flavonoids, and organic acids. Compared to the control group (C), calves in the SQBQP-H (high dose) and SQBQP-L (low dose) groups showed a significant increase in serum amylase (AMS) levels (P<0.001), while lipase content significantly decreased (P<0.05). Additionally, the average daily gain, T-AOC, and cellulase content of calves in the SQBQP-H group significantly increased (P<0.05). Proteobacteria and Succinivibrio in the rumen flora of the SQBQP-H group was significantly lower than that of the C group (P<0.05). The relative abundance of Proteobacteria, Actinobacteria, Candidatus_Saccharibacteria, Deinococcus_Thermus, Cyanobacteria, and Succinivibrio in the SQBQP-H group was significantly increased (P<0.05), while the relative abundance of Tenericutes and Oscillibacter was significantly decreased (P<0.05). Serum metabolomics analysis revealed 20 differential metabolites, mainly enriched in amino acid biosynthesis, β-alanine metabolism, tyrosine, and tryptophan biosynthesis metabolic pathways (P<0.05). Correlation analysis results showed that Butyrivibrio in rumen flora and Oscillibacter_valericigenes in intestinal flora were significantly positively correlated with average daily gain, serum biochemical indexes, and differential metabolite (-)-Epigallocatechin (R>0.58, P<0.05). SQBQP can promote calves weight gain and enhance health by modulating gastrointestinal flora and metabolic processes in the body.

Transcriptome and Metabolome Jointly Revealed the Regulation and Pathway of Flower and Pod Abscission Caused by Shading in Soybean (Glycine max L.)

Flowers and pod abscission significantly reduces soybean yield. This study aims to identify the main signaling pathways and key candidate genes in soybean leaves that affect flower and pod abscission under shade conditions. This information will be useful for the localization and cloning of genes related to abscission. Two soybean cultivars with different abscission rates (Liaodou 32 and Shennongdou 28) were used in this experiment. The soybean leaves were subjected to 50% shading treatment and the transcriptome and metabolome was sequenced during the light-sensitive period. The effects of weak light at different growth stages on the metabolic pathways of soybean leaves and organ abscission were investigated by analyzing plant phenotype and physiological changes. The results showed that both two cultivars triggered the same molecular mechanism and similar metabolite accumulation mode by shading, but the regulations of the two cultivars were different. The key candidate genes identified for soybean flower and pod abscission caused by shading were DIV, MYB06, MYB44, MY1R1, MYBS3, WRKY6, WRK53, WRK70, WRK40, DOF14, CDF3, CDF2, GATA5, DREB3 and ERF3; the differentially expressed genes that caused the variation between the cultivars were SRM1, MYB16, WRK24, COL16, MYB61 and TRB1. The main metabolic pathways involved in soybean flower and pod abscission caused by shading were secondary metabolite biosynthesis pathway, metabolic pathway, cofactor biosynthesis pathway, phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, fatty acid biosynthesis pathway and amino acid biosynthesis pathway; the DEMs that caused the differences among the cultivars were carbon metabolism, glutathione metabolism, biotin metabolism, nucleotide metabolism, purine metabolism, plant hormone signaling, flavone and flavonol biosynthesis, lysine degradation, arginine and proline metabolism, amino sugars and nucleotide sugars metabolism, etc. In conclusion, shading treatment in the light-sensitive period of soybean changed the physiological response and gene expression level of leaves, inhibited carbohydrate metabolism and transport and biosynthesis of secondary metabolites, and thereby leading to increased competition and hormonal disruption, which promoted the abscission of soybean flowers/pods and reduced grain yield.

Metabolomics Analysis of Sodium Salicylate Improving the Preservation Quality of Ram Sperm.

The aim of this study was to investigate the effects of sodium salicylate (SS) on the preservation and metabolic regulation of sheep sperm. Under 4 °C low-temperature conditions, SS (at 10 µM, 20 µM, 30 µM, and 50 µM) was added to the semen diluent to detect sperm motility, plasma membrane, and acrosome integrity. Based on the selected optimal concentration of SS (20 µM), the effects of 20 µM of SS on sperms' antioxidant capacity and mitochondrial membrane potential (MMP) were evaluated, and metabolomics analysis was conducted. The results showed that on the 20th day of low-temperature storage, the sperm motility of the 20 µM SS group was 62.80%, and the activities of catalase (CAT) and superoxide dismutase (SOD) were significantly higher than those of the control group (p < 0.01). The content of Ca2+, reactive oxygen species (ROS), and malondialdehyde (MDA) were significantly lower than those of the control group (p < 0.01), and the total antioxidant capacity (T-AOC) was significantly higher than that of the control group (p < 0.05); mitochondrial activity and the total cholesterol (TC) content were significantly higher than those in the control group (p < 0.01). An ultrastructural examination showed that in the SS group, the sperm plasma membrane and acrosome were intact, the fibrous sheath and axoneme morphology of the outer dense fibers were normal, and the mitochondria were arranged neatly. In the control group, there was significant swelling of the sperm plasma membrane, rupture of the acrosome, and vacuolization of mitochondria. Using metabolomics analysis, 20 of the most significant differential metabolic markers were screened, mainly involving 6 metabolic pathways, with the amino acid biosynthesis pathway being the most abundant. In summary, 20 µM of SS significantly improved the preservation quality of sheep sperm under low-temperature conditions of 4 °C.

The SLC38A9–mTOR axis is involved in autophagy in the juvenile yellow catfish (Pelteobagrus fulvidraco) under ammonia stress

The primary objective of this study was to examine the effect of acute ammonia stress on hepatic physiological alterations in yellow catfish by performing a comprehensive analysis of the metabolome and transcriptome. The present study showed that ammonia stress led to liver metabolic disruption, functional incapacitation, and oxidative damage. Transcriptomic and metabolomic analyses revealed transcriptional and metabolic differences in the liver of yellow catfish under control and high ammonia stress conditions. After 96 h of acute exposure to ammonia, the mRNA levels of 596 liver genes were upregulated, whereas those of 603 genes were downregulated. Enrichment analysis of the differentially expressed genes identified multiple signalling pathways associated with autophagy, including the endocytosis, autophagy-animal, and mammalian target of rapamycin signalling pathways. A total of 186 upregulated and 117 downregulated metabolites, primarily associated with amino acid biosynthesis pathways, were identified. Multi-omics integration revealed the solute carrier family 38 member 9 (SLC38A9)-mammalian target of rapamycin axis as a signalling nexus for amino acid-mediated modulation of autophagy flux, and q-PCR was used to assess the expression of autophagy-related genes (LC3a and sqstm1), revealing an initial inhibition followed by the restoration of autophagic flux during ammonia stress. Subsequent utilisation of arginine as a specific SLC38A9 activator during ammonia stress demonstrated that augmented SLC38A9 expression hindered autophagy, exacerbated ammonia toxicity, and caused a physiological decline (total cholesterol, total triglyceride, acid phosphatase, alkaline phosphatase, aspartate aminotransferase, and alanine aminotransferase levels were significantly increased), oxidative stress, and apoptosis. Autophagy activation may be an adaptive mechanism to resist ammonia stress.