NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants.

NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. The number of human lncRNAs has increased from 172 216 to 173 112. The number of mouse lncRNAs increased from 131 697 to 131 974. The number of plant lncRNAs is 94 697. The relationship between lncRNAs in human and cancer were updated with transcriptome sequencing profiles. Three important new features were also introduced in NONCODEV6: (i) updated human lncRNA-disease relationships, especially cancer; (ii) lncRNA annotations with tissue expression profiles and predicted function in five common plants; iii) lncRNAs conservation annotation at transcript level for 23 plant species. NONCODEV6 is accessible through http://www.noncode.org/.

CcMYB12 Positively Regulates Flavonoid Accumulation during Fruit Development in Carya cathayensis and Has a Role in Abiotic Stress Responses.

Flavonoid, an important secondary metabolite in plants, is involved in many biological processes. Its synthesis originates from the phenylpropane metabolic pathway, and it is catalyzed by a series of enzymes. The flavonoid biosynthetic pathway is regulated by many transcription factors, among which MYB transcription factors are thought to be key regulators. Hickory (Carya cathayensis) is an economic forest tree species belonging to the Juglandaceae family, and its fruit is rich in flavonoids. The transcriptome of exocarp and seed of hickory has previously been sequenced and analyzed by our team, revealing that CcMYB12 (CCA0691S0036) may be an important regulator of flavonoid synthesis. However, the specific regulatory role of CcMYB12 in hickory has not been clarified. Through a genome-wide analysis, a total of 153 R2R3-MYB genes were identified in hickory, classified into 23 subclasses, of which CcMYB12 was located in Subclass 7. The R2R3-MYBs showed a differential expression with the development of hickory exocarp and seed, indicating that these genes may regulate fruit development and metabolite accumulation. The phylogenetic analysis showed that CcMYB12 is a flavonol regulator, and its expression trend is the same as or opposite to that of flavonol synthesis-related genes. Moreover, CcMYB12 was found to be localized in the nucleus and have self-activation ability. The dual-luciferase reporter assay demonstrated that CcMYB12 strongly bonded to and activated the promoters of CcC4H, CcCHS, CcCHI, and CcF3H, which are key genes of the flavonoid synthesis pathway. Overexpression of CcMYB12 in Arabidopsis thaliana could increase the content of total flavonoids and the expression of related genes, including PAL, C4H, CHS, F3H, F3'H, ANS, and DFR, in the flavonoid synthesis pathway. These results reveal that CcMYB12 may directly regulate the expression of flavonoid-related genes and promote flavonoid synthesis in hickory fruit. Notably, the expression level of CcMYB12 in hickory seedlings was significantly boosted under NaCl and PEG treatments, while it was significantly downregulated under acid stress, suggesting that CcMYB12 may participate in the response to abiotic stresses. The results could provide a basis for further elucidating the regulation network of flavonoid biosynthesis and lay a foundation for developing new varieties of hickory with high flavonoid content.

Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.).

Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole-genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome-wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.

Alterations of estradiol-induced histone H3 acetylation in the preoptic area and anteroventral periventricular nucleus of middle-aged female rats.

In this study we investigated the characteristics of histone H3 acetylation in the anterior hypothalamus under E2 positive feedback to gain a better understanding of the mechanism underlying reduced GnRH neuron activation and altered gene expression in female reproductive aging. Young and middle-aged female rats were ovariectomized (OVX) and treated with estradiol (E2) or oil. C-Fos expression, the number of GnRH neurons co-localized with c-Fos in the preoptic area (POA), and the number of acetylated histone H3 cells in the POA and anteroventral periventricular nucleus (AVPV) were quantified at the time of the expected GnRH neuron activation. We used real-time PCR to evaluate the expression of Esr1 target genes including Kiss1 and VGluT2 and genes known as Esr1 coregulators in the anterior hypothalamus. Our results show that in the young females, E2 markedly increased histone H3 acetylation in the POA and AVPV, coincident with increased c-Fos and GnRH neuron activation in the POA. In middle-aged females, E2-induced histone H3 acetylation was reduced in the POA but was not significantly altered in the AVPV. This occurred in association with a reduction of c-Fos expression and the number of GnRH cells expressing c-Fos in the POA as well as a down-regulation of Kiss1 and VGluT2 mRNA expression in the anterior hypothalamus of the animals. E2 caused significant decreases in Ncoa2 and Crebbp mRNA expression in the anterior hypothalamus of young, but not middle-aged females. Taken together, these data suggest that alterations of histone H3 acetylation in the POA and AVPV and the inability of Ncoa2 and Crebbp to respond to E2 in the middle-aged anterior hypothalamus partially contribute to the decline of GnRH neuron activation and E2 target gene expression changes that occur in female along with reproductive aging.

Identification and profiling of conserved and novel microRNAs involved in oil and oleic acid production during embryogenesis in Carya cathayensis Sarg.

MicroRNAs (miRNAs) are important regulators of plant development and fruit formation. Mature embryos of hickory (Carya cathayensis Sarg.) nuts contain more than 70% oil (comprising 90% unsaturated fatty acids), along with a substantial amount of oleic acid. To understand the roles of miRNAs involved in oil and oleic acid production during hickory embryogenesis, three small RNA libraries from different stages of embryogenesis were constructed. Deep sequencing of these three libraries identified 95 conserved miRNAs with 19 miRNA*s, 7 novel miRNAs (as well as their corresponding miRNA*s), and 26 potentially novel miRNAs. The analysis identified 15 miRNAs involved in oil and oleic acid production that are differentially expressed during embryogenesis in hickory. Among them, nine miRNA sequences, including eight conserved and one novel, were confirmed by qRT-PCR. In addition, 145 target genes of the novel miRNAs were predicted using a bioinformatic approach. Our results provide a framework for better understanding the roles of miRNAs during embryogenesis in hickory.

In vitro gene expression and mRNA translocation from transformed walnut (Juglans regia) rootstocks expressing DsRED fluorescent protein to wild-type scions.

KEY MESSAGE: An in vitro grafting method was developed for examining gene translocation from rootstock to scion in walnut. Results showed the DsRED gene itself was not translocated but expressed mRNA was. Grafting is widely used in plants, especially in fruit and nut crops. Selected rootstocks can control scion growth and physiological traits, including shortening of the juvenile phase and controlling tree size. Rootstocks also can provide improved soil adaptation and pathogen resistance. Development of genetically modified (GM) fruit crops has progressed recently, but commercial cultivation is still limited due to the time required for evaluation and issues with deregulation. In this study, we evaluated the stability of DsRED marker gene expression in in vitro walnut shoots and examined translocation of the gene and its mRNA from transformed rootstock to wild-type scion. Results show that DsRED was expressed uniformly in transformed tissue-cultured shoots. When used as in vitro rootstocks, these had good graft affinity with wild-type control scion. PCR and qRT-PCR analysis showed that the DsRED gene was not transported from rootstock to scion, but the transcribed mRNA was translocated. This result provides further evidence of gene signal transport from rootstock to scion in fruit and nut crops.

Genome-wide comparative analysis of LEAFY promoter sequence in angiosperms.

Regulation of the flowering mechanism is influenced by many environmental factors. Dissecting the regulatory processes upstream of the LFY (LEAFY) gene will help us to understand the molecular mechanisms of floral induction. In total, 53 LFY sequences were identified in 37 species. Among the 53 selected LFY promoters and after eliminating the short sequences, 47 LFY promoters were analyzed. Comparative genome studies for LFY promoters among plants showed that TATA-box existed in all herbaceous plants. The 1345-bp promoter sequence upstream to hickory LFY gene was cloned and analyzed, together with functional studies. The result of sequence alignment showed that the region of the hickory LFY promoter has only two conserved auxin response elements (AuxRE), whereas other plants had four. The positions of AuxRE in hickory and walnut were the same, but they were different from the positions from other plants. Furthermore the sequence analysis showed that the promoter have TATA-box and CAAT-box motifs. Deletion analysis of these motifs did not block ß-glucuronidase (GUS) activity during the transient expression assay, suggesting that it may be a TATA-less promoter. Low temperature and light significantly induced the full-length promoter to increase about two folds of the GUS enzymatic activity, suggesting these environmental factors induced flowering in hickory.

The mechanism of high contents of oil and oleic acid revealed by transcriptomic and lipidomic analysis during embryogenesis in Carya cathayensis Sarg.

BACKGROUND: Hickory (Carya cathayensis Sarg.) accumulates more than 70% oil and 90% unsaturated fatty acids with considerably high oleic acid in its mature embryo. The concurrent global trancriptomic and lipidomic analyses provided a framework for better understanding of glycerolipid biosynthesis and metabolism in the hickory nut. RESULTS: The synthetical regulation of numerous leading lipid-related genes harmonized with the oil accumulation and fatty acid conversion in embryo development. The high level of ACCase correlated positively with fatty acids de novo synthesis, and the synergy of DGAT2 and PDAT promoted the TAG assembly, and oleosins, caleosins and steroleosins were transcribed considerably high for timely energy reserve in oil body. Glycolysis possibly provided sufficient precursors and energy for lipid synthesis. The perfect harmonization of the high level of SAD with low level of FAD2 facilitated the oleic acid accumulation. And the ratio of FATA/FATB or SAD/FATB was proposed for determining the saturated degree of oil. The gene multi-copy event was generated probably for accommodating various survival environments. A thermotolerant defense system including TAG hydrolysis determinants, heat shock proteins, and high ratio of MUFA to PUFA constrained the lipid degradation and provided a guarantee for high lipid content. A batch of potential genes recruited from the co-expression network helps us to understand the lipid synthesis and the response to high temperature better. CONCLUSIONS: The high transcriptional levels of key genes in lipid synthesis promoted the oil accumulation, and the harmonious expression of key ones for unsaturated fatty acids led oleic acid to high levels.

Identification of microRNAs differentially expressed involved in male flower development.

Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees.

A long downstream probe-based platform for multiplex target capture.

A simple and rapid detection platform was established for multiplex target capture through generating single-strand long downstream probe (ssLDP), which was integrated with the ligase detection reaction (LDR) method for the purpose of multiplicity and high specificity. To increase sensitivity, the ladder-like polymerase chain reaction (PCR) amplicons were generated by using universal primers that complement ligated products. Each of the amplicons contained a stuffer sequence with a defined yet variable length. Thus, the length of the amplicon is an index of the specific suppressor, allowing its identification via electrophoresis. The multiplexed diagnostic platform was optimized using standard plasmids and validated by using potato virus suppressors as a detection model. This technique can detect down to 1.2 × 10(3) copies for single or two mixed target plasmids. When compared with microarray results, the electrophoresis showed 98.73-100% concordance rates for the seven suppressors in the 79 field samples. This strategy could be applied to detect a large number of targets in field and clinical surveillance.

Development of SSR Markers in Hickory (Carya cathayensis Sarg.) and Their Transferability to Other Species of Carya.

Hickory (Carya cathayensis Sarg.), an important nut-producing species in Southeastern China, has high economic value, but so far there has been no cultivar bred under species although it is mostly propagated by seeding and some elite individuals have been found. It has been found recently that this species has a certain rate of apomixis and poor knowledge of its genetic background has influenced development of a feasible breeding strategy. Here in this paper we first release SSR (Simple sequence repeat) markers developed in this species and their transferability to other three species of the same genus, Carya. A total of 311 pairs of SSR primers in hickory were developed based on sequenced cDNAs of a fruit development-associated cDNA library and RNA-seq data of developing female floral buds and could be used to distinguish hickory, C. hunanensis Cheng et R. H. Chang ex R. H. Chang et Lu, C. illinoensis K. Koch (pecan) and C. dabieshanensis M. C. Liu et Z. J. Li, but they were monomorphic in both hickory and C. hunanensis although multi-alleles have been identified in all the four species. There is a transferability rate of 63.02% observed between hickory and pecan and the markers can be applied to study genetic diversity of accessions in pecan. When used in C. dabieshanensis, it was revealed that C. dabieshanensis had the number of alleles per locus ranging from 2 to 4, observed heterozygosity from 0 to 0.6667 and expected heterozygosity from 0.333 to 0.8667, respectively, which supports the existence of C. dabieshanensis as a separate species different from hickory and indicates that there is potential for selection and breeding in this species.

Effect of 26 years of intensively managed Carya cathayensis stands on soil organic carbon and fertility.

Chinese hickory (Carya cathayensis), a popular nut food tree species, is mainly distributed in southeastern China. A field study was carried out to investigate the effect of long-term intensive management on fertility of soils under a C. cathayensis forest. Results showed that after 26 years' intensive management, the soil organic carbon (SOC) content of the A and B horizons reduced by 19% and 14%, respectively. The reduced components of SOC are mainly the alkyl C and O-alkyl C, whereas the aromatic C and carbonyl C remain unchanged. The reduction of active organic matter could result in degradation of soil fertility. The pH value of soil in the A horizon had dropped by 0.7 units on average. The concentrations of the major nutrients also showed a decreasing trend. On average the concentrations of total nitrogen (N), phosphorus (P), and potassium (K) of tested soils dropped by 21.8%, 7.6%, and 13.6%, respectively, in the A horizon. To sustain the soil fertility and C. cathayensis production, it is recommended that more organic fertilizers (manures) should be used together with chemical fertilizers. Lime should also be applied to reduce soil acidity.

Characteristic analysis of BZR genes family and their responses to hormone treatments and abiotic stresses in Carya illinoinensis.

As the core of Brassinosteroids (BR) signaling pathway, BR-resistant (BZR) transcription factor regulates thousands of targeted genes mediating photomophogenesis, pollen sterility, cell expansion and stress response. Pecan (Carya illinoinensis) is a famous trees species of Carya, and its nut has high nutritional and economic values. However, there has no report on BZR genes family in pecan yet. Herein, totals of seven CiBZR members were identified in pecan genome, which were predicted to be hydrophilic unstable proteins and located in the nucleus. CiBZR genes had close evolutionary relationships with CcBZRs and JrBZRs in both Carya cathayensis and Juglans regia. These seven CiBZR genes were located independently on 7 chromosomes without doubling or tandem duplication. Based on the analysis of conserved motifs and gene structures, CiBZR genes were divided into three categories. More than 40 cis-acting elements were found in the 2 kb promoter regions of CiBZRs, which were mainly involved in hormone, light, and stress response, and plant growth and development. Notably, some of these CiBZR proteins were mainly located in the nucleus, had the self-activation ability and interaction relationship with BIN2 kinase, and negatively regulated the expression of CiCPD and CiDWF4. Gene expressions analysis further showed that CiBZR genes could express in many tissues and shared similar expression trends during embryo development. Moreover, most CiBZR genes responded to BR, Gibberellin (GA), Strigolactone (SL), salt, acid and osmotic stress. This study provides theoretical basis for the subsequent study on the role of CiBZR family genes in plant growth, development and stress responses.

Polyphenols from hickory nut reduce the occurrence of atherosclerosis in mice by improving intestinal microbiota and inhibiting trimethylamine N-oxide production.

BACKGROUND: Trimethylamine N-oxide (TMAO), a metabolite produced by intestinal microbiota through metabolizing phosphatidylcholine, choline, l-carnitine and betaine in the diet, has been implicated in the pathogenesis of atherosclerosis (AS). Concurrently, dietary polyphenols have garnered attention for their potential to ameliorate obesity, diabetes and atherosclerosis primarily by modulating the intestinal microbial structure. Hickory (Carya cathayensis) nut, a polyphenol-rich food product favored for its palatability, emerges as a candidate for exploration. HYPOTHESIS/PURPOSE: The relationship between polyphenol of hickory nut and atherosclerosis prevention will be firstly clarified, providing theoretical basis for the discovery of natural products counteracting TMAO-induced AS process in hickory nut. STUDY DESIGN AND METHODS: Employing Enzyme-linked Immunosorbent Assay (ELISA) and histological examination of aortic samples, the effects of total polyphenol extract on obesity index, inflammatory index and pathological changes of atherosclerosis in C57BL/6 J mice fed with high-fat and high choline diet were evaluated. Further, the composition, abundance, and function of mouse gut microbiota were analyzed through 16srDNA sequencing. Concurrently, the levels of TMAO and the expression of key enzymes (CutC and FMO3) involved in its synthesis are quantified using ELISA, Western Blot and Real-Time Quantitative PCR (RT-qPCR). Additionally, targeted metabolomic profiling of the hickory nut polyphenol extract was conducted, accompanied by molecular docking simulations to predict interactions between candidate polyphenols and the CutC/FMO3 using Autodock Vina. Finally, the docking prediction were verified by microscale thermophoresis (MST) . RESULTS: Polyphenol extracts of hickory nut improved the index of obesity and inflammation, and alleviated the pathological changes of atherosclerosis in C57BL/6 J mice fed with high-fat and high-choline diet. Meanwhile, these polyphenol extracts also changed the composition and function of intestinal microbiota, and increased the abundance of microorganisms in mice. Notably, the abundance of intestinal microbiota endowed with CutC gene was significantly reduced, coherent with expression of CutC catalyzing TMA production. Moreover, polyphenol extracts also decreased the expression of FMO3 in the liver, contributing to the reduction of TMAO levels in serum. Furthermore, metabonomic profile analysis of these polyphenol extracts identified 647 kinds of polyphenols. Molecular docking predication further demonstrated that Casuariin and Cinnamtannin B2 had the most potential inhibition on the enzymatic activities of CutC or FMO3, respectively. Notably, MST analysis corroborated the potential for direct interaction between CutC enzyme and available polyphenols such as Corilagin, (-)-Gallocatechin gallate and Epigallocatechin gallate. CONCLUSION: Hickory polyphenol extract can mitigate HFD-induced AS by regulating intestinal microflora in murine models. In addition, TMA-FMO3-TMAO pathway may play a key role in this process. This research unveils, for the inaugural time, the complex interaction between hickory nut-derived polyphenols and gut microbial, providing novel insights into the role of dietary polyphenols in AS prevention.

Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.).

BACKGROUND: Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis. RESULTS: Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better. CONCLUSIONS: Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC' model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.

Purification and enzymatic characterization of alcohol dehydrogenase from Arabidopsis thaliana.

Alcohol dehydrogenases (ADH) catalyze the interconversion between alcohols and aldehydes with the reduction of nicotinamide adenine dinucleotide (NAD(+)) to NADH. In this study, for the first time we report an over-expression and purification strategy for the Arabidosis thaliana ADH (AtADH), and characterize its enzymatic properties. AtADH was expressed in an Escherichia coli system, the polyhistidine-tag was removed after the recombinant AtADH protein was purified by metal chelating affinity chromatography. Activity assays demonstrated that AtADH has distinct enzymatic properties when compared with many well-known ADHs. It held peak activity at pH 10.5 and showed broad substrate selectivity for primary and secondary alcohols. The kinetic Km parameters for both ethanol and coenzyme were in the order of mM. This relative low affinity may reflect the need of the plant to maintain a supply of NAD(+) in nature. Different from yeast ADH, AtADH showed almost the same activity for short straight chain alcohols and reduced activity for secondary alcohols. This broad spectrum in alcohol selection and the observed higher catalytic activity (high Vmax (EtOH)) may result from the requirement of the single enzyme to accommodate many substrates.

Food-Derived Peptides: Beneficial CNS Effects and Cross-BBB Transmission Strategies.

Food-derived peptides, as dietary supplements, have significant effects on promoting brain health and relieving central nervous system (CNS) diseases. However, the blood-brain barrier (BBB) greatly limits their in-brain bioavailability. Thus, overcoming the BBB to target the CNS is a major challenge for bioactive peptides in the prevention and treatment of CNS diseases. This review discusses improvement in the neuroprotective function of food-derived active peptides in CNS diseases, as well as the source of BBB penetrating peptides (BBB-shuttles) and the mechanism of transmembrane transport. Notably, this review also discusses various peptide modification methods to overcome the low permeability and stability of the BBB. Lipification, glycosylation, introduction of disulfide bonds, and cyclization are effective strategies for improving the penetration efficiency of peptides through the BBB. This review provides a new prospective for improving their neuroprotective function and developing treatments to delay or even prevent CNS diseases.

Gut microbiota and metabolites in estrus cycle and their changes in a menopausal transition rat model with typical neuroendocrine aging.

Background: Neuroendocrine alterations in the mid-life hypothalamus coupled with reproductive decline herald the initiation of menopausal transition. The certain feature and contribution of gut microflora and metabolites to neuroendocrine changes in the menopausal transition remain largely unknown. Methods: Fecal samples of rats experiencing different reproductive stages were collected and processed for 16S rRNA and liquid chromatography-mass spectrometry sequencing. The differences of gut microbiota and metabolites between young and middle-aged rats during proestrus and diestrus were analyzed, and their relationships to neuroendocrine aging were then examined. Results: At the genus level, Anaeroyorax, Rikenella, Tyzzerella_3, and Atopostipes were abundant at proestrus, while Romboutsia, Turicibacter, Clostridium_sensu_stricto_1, Ruminococcaceae_NK4A214_group, CHKCI002, Ruminococcaceae_UCG-010, Staphylococcus, Family_XII_AD3011_group, Ruminococcaceae UCG-011, and Christensenellaceae_R_7_group were enriched in the diestrus of middle-aged rats. DNF00809, Phocea, and Lachnospiraceae_UCG-006 were found abundant during proestrus instead, while Bacteroides, Lactobacillus, Erysipelatoclostridium, Anaeroplasma, Anaerofustis, Parasutterella, and Enterococcus were enriched at the diestrus of young female individuals. Discriminatory metabolites were identified involving 90 metabolic pathways among the animal sets, which were enriched for steroid hormone biosynthesis, arachidonic metabolism, primary bile acid synthesis, and ovarian steroidogenesis. A total of 21 metabolites lacking in hormone-associated changes in middle-aged female individuals presented positive or negative correlations with the circulating luteinizing hormone, bile acid, fibroblast growth factor 19, and gut hormones. Moreover, close correlations were detected between the intestinal bacteria and their metabolites. Conclusion: This study documents specific gut microbial composition changes and concomitant shifting trends of metabolites during menopausal transition, which may initiate the gut-brain dysfunction in neuroendocrine aging.