Search Results (9,093)

This study aimed to elucidate the molecular mechanisms underlying phenotypic divergence between two Lentinula edodes strains, Le_L and Le_S, which exhibit distinct fruiting body morphologies. While phenotypic variation among mushroom strains has been widely observed, the relative contributions of transcriptional regulation and structural genomic variation to these differences remain poorly understood. Comparative transcriptome analysis identified 8541 differentially expressed genes (DEGs), revealing clear functional divergence between the two strains. Genes upregulated in Le_S were predominantly enriched in ribosomal components and translation-related processes, indicating enhanced protein synthesis activity. In contrast, Le_L-upregulated genes were associated with transporters, transcription factors, and diverse metabolic pathways, suggesting broader regulatory and physiological functions. Protein–protein interaction network analysis further highlighted distinct regulatory architectures, with ribosomal proteins forming highly interconnected hub gene modules in Le_S, whereas Le_L hub genes were functionally diverse and included multiple members of the Major Facilitator Superfamily (MFS). Ortholog analysis across 33 L. edodes strains demonstrated that most hub genes were conserved, indicating their roles as core genetic components. Despite widespread genome-wide variation, including 7931 SNPs and 1149 INDELs, sequence variation within hub genes was limited, and allele-specific expression analysis revealed no significant allelic imbalance. In contrast, presence–absence variation (PAV) analysis identified structural differences affecting MFS transporter genes, which were absent in Le_S but present and upregulated in Le_L. Collectively, these findings suggest that structural genomic variation, particularly involving transporter genes, may play a more prominent role than sequence-level variation in driving phenotypic divergence. This study provides new insights into the genetic basis of strain-specific traits in L. edodes and highlights the importance of integrating multi-level genomic analyses. Full article

Background: Postmenopausal osteoporosis is a common metabolic bone disorder characterized by decreased bone mass and microstructural deterioration, often accompanied by increased bone marrow adiposity and systemic fat accumulation. Kun-Ling Wan Formula (KLW) is a compound Chinese medicine clinically used for gynecological disorders, though its effects on postmenopausal osteoporosis and associated fat accumulation remain unclear. Distinct from previous herbal formulation studies that primarily focused on bone outcomes, our study uniquely integrates bone protection, marrow adiposity reduction, systemic metabolic improvement, and multi-omics mechanistic dissection in a high-fat diet-fed ovariectomized mouse model. Methods: KLW chemical composition was analyzed by UPLC-Q-TOF/MS. Ovariectomized (OVX) C57BL/6J mice fed high-fat or normal diet were treated with KLW at clinically equivalent or double doses, with estrogen and active compounds as controls. Bone microstructure was assessed by micro-CT, bone marrow fat by MRI-PDFF, and metabolism by OGTT, ITT, and metabolic cages. Network pharmacology, proteomics, molecular docking, and dynamics simulations identified core targets. C3H10T1/2 cells were used to assess osteogenic/adipogenic differentiation and mTOR pathway activation. Results: Twelve compounds were identified in KLW. In OVX mice, KLW significantly improved bone mineral density and trabecular microstructure, reduced adiposity and bone marrow fat, and enhanced glucose tolerance and insulin sensitivity. In vitro, KLW promoted osteogenesis and suppressed adipogenesis in C3H10T1/2 cells. Integrative analyses identified mTOR as a central target, with chrysophanol, pyrogallol, and apigenin showing high-affinity binding. KLW inhibited mTOR/S6K phosphorylation during differentiation, an effect reversible by leucine. Conclusions: KLW ameliorates osteoporosis and reduces fat accumulation in OVX mice by shifting mesenchymal stem cell differentiation toward osteogenesis via mTOR pathway modulation. Full article

Background: Research indicates that hepatic gluconeogenesis mediates metabolic coupling between the liver and muscles via the Cori cycle and participates in liver–brain axis communication through its metabolic products and regulatory networks, thereby linking it to the pathogenesis of depression. Together, these mechanisms form the molecular basis for the antidepressant effects of exercise-regulated hepatic gluconeogenesis. Regular exercise promotes skeletal muscle contraction, causing the muscles to release more lactate into the circulatory system. Lactate acts as a substrate for gluconeogenesis and activates downstream signaling pathways, thereby enhancing the gluconeogenic response. During exercise, glycogenolysis directly provides energy, while lactate produced by glycolysis enters the liver via the Cori cycle to serve as a substrate for gluconeogenesis. By maintaining blood glucose homeostasis, this process ensures a stable energy supply to the brain, thereby improving cognitive and emotional functions. This study aims to elucidate how key substrates, regulatory factors, and rate-limiting enzymes involved in hepatic gluconeogenesis and exercise influence brain energy supply, cognitive function, and emotional regulation during depression. It seeks to identify the potential targets and mechanisms through which exercise exerts its antidepressant effects via hepatic gluconeogenesis, with the goal of providing a theoretical foundation for research into the mechanisms of depression and for clinical exercise interventions. Methods: This review conducted a comprehensive search of the recent literature on exercise, hepatic gluconeogenesis, and depression in major domestic and international databases. Adopting an interdisciplinary approach that integrates hepatic gluconeogenesis and exercise, it synthesizes existing evidence to explore the metabolic mechanisms by which exercise improves depression through the regulation of hepatic gluconeogenesis pathways. Results: Research has found that exercise may modulate hepatic gluconeogenic substrates and regulate the expression of cAMP-responsive element-binding protein in states of depression, regulatory factors such as liver kinase B1, forkhead box protein 01, hepatocyte nuclear factor 4 alpha, and peroxisome proliferator activated receptor gamma co activator factor 1 alpha are used to affect key rate limiting enzymes of hepatic gluconeogenesis, such as phosphoenolpyruvate carboxykinase and glucose-6-phosphatase, enhance hepatic gluconeogenesis processes, maintain blood glucose homeostasis, ensure brain energy supply, and improve depression. Conclusions: Exercise intervention targeting hepatic gluconeogenesis may be a potential therapeutic strategy for depression. Full article

Background: The coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, remains a significant threat to global health. This continued threat is due to the emergence of new variants, the immune system’s limited ability to respond, and the limited effectiveness of available treatments for all individuals. Therefore, leveraging drug repurposing, a fast and inexpensive way to find other drugs that have already been shown to be safe and efficacious, becomes useful. This study leverages ADMET profiling, network pharmacology, and molecular docking to evaluate the repurposing of Product Nkabinde for COVID-19 treatment. Methods: ADMET analysis involving the bioactive phytochemicals of PN was evaluated for pharmacokinetic appropriateness and drug-likeness. Using topological analysis, a network of protein–protein interactions was built to identify hub genes, and predicted compound targets were intersected with COVID-19-associated genes to find shared targets. Their biological importance was characterized using functional enrichment analysis. The binding affinities of PN phytochemicals against hub proteins and SARS-CoV-2 viral proteases (Mpro and PLpro) were assessed by molecular docking using AutoDock Vina. To confirm docking accuracy, co-crystallized ligands were redocked using Schrodinger 2022-1. The multi-target therapeutic potential of PN in COVID-19 was assessed using this integrative network pharmacology and molecular docking technique. Results: Molecular docking demonstrated that PN phytochemicals displayed robust and persistent binding affinities for both viral and host targets. Oleanolic acid showed the best affinity toward Mpro (−12.9 kcal/mol vs. −8.3 kcal/mol), while quercetin-3-O-β-D-(6′-galloyl)-glucopyranoside showed better binding to PLpro (−8.4 kcal/mol vs. −6.4 kcal/mol). Procyanidin B2 toward HCK (−10.5 vs. −7.9 kcal/mol), diosgenin toward EGFR (−9.4 vs. −8.4 kcal/mol), rutin toward SRC (−10.5 vs. −7.8 kcal/mol), and pimelea factor P2 toward PIK3R1 (−11.0 vs. −8.2 kcal/mol) all showed significantly higher affinities than their corresponding co-crystallized ligands. Furthermore, procyanidin B2 demonstrated consistent binding to STAT1 and STAT3, confirming its role in modulating immune signals. Most of the PN phytochemicals show advantageous pharmacokinetic properties, including elevated anticipated gastrointestinal absorption and adherence to Lipinski’s rule of five, signifying favorable oral bioavailability and drug-like properties. Moreover, PN exhibits a remarkable multi-target binding capacity against both SARS-CoV-2 proteases and key host signaling proteins involved in immune regulation and inflammatory responses, as determined by this integrative network pharmacology and molecular docking investigation. Conclusions: PN’s prospects as a host-directed, antiviral treatment for COVID-19 are demonstrated by its coordinated modulation of the PI3K/AKT, JAK–STAT, SRC-family kinase, EGFR, and SYK pathways. These results necessitate further experimental and clinical validation, providing a solid computational basis for repurposing PN in the treatment of COVID-19. Full article

This study employs molecular dynamics simulations to investigate the condensation behavior of water molecules on hydrophilic/hydrophobic substrates under varying electric field strengths. It reveals the synergistic regulation effect between electric field strength and surface wettability from the perspectives of condensation rate and morphological evolution. The results indicate that the condensation rate on hydrophilic surfaces first increases and then decreases with increasing electric field strength; the condensation efficiency reaches its maximum at an electric field strength of 1.6 V/nm. Conversely, the condensation efficiency on hydrophobic surfaces shows a monotonically decreasing trend with increasing electric field strength; the presence of an electric field does not facilitate condensation on hydrophobic surfaces. The orientation of water molecule dipole moments is synergistically regulated by external electric fields, intermolecular interactions, and substrate–water interactions. The weaker the wettability, the more readily the electric field assumes a dominant role. Furthermore, the electric field induces parallel alignment of dipole moments along its direction, enhancing intermolecular attractions along the electric field axis (Z-axis). This also drives the reconfiguration of hydrogen-bond networks, ultimately leading to the aggregation of water molecules into clusters aligned with the electric field, thereby transforming the condensation morphology. Full article

Hypertension is a severe global public health issue. Food-derived angiotensin-converting enzyme (ACE)-inhibitory peptides have shown great potential as safe and effective alternatives to synthetic antihypertensive drugs. Camel milk is rich in bioactive peptides. This study aimed to screen for ACE-inhibitory peptides from hydrolyzed camel casein, explore their inhibitory mechanisms and endothelial protective effects in vitro, and reveal their potential antihypertensive pathways using network pharmacology. This study screened three peptides with angiotensin-converting enzyme (ACE) inhibitory activity from enzymatically hydrolyzed camel casein components: MVPFLQPK, VPFLQPKVM, and QKWKFL, with IC₅₀ values of 277.1, 396.9, and 486.9 μmol/L, respectively. Enzyme inhibition kinetics analysis indicated that MVPFLQPK exhibited a non-competitive inhibition pattern, VPFLQPKVM exhibited a mixed inhibition pattern, and QKWKFL exhibited a competitive inhibition pattern. Molecular docking revealed that all three peptides formed hydrogen bond interactions with ACE, and QKWKFL and VPFLQPKVM directly bound to the enzyme’s active site to inhibit substrate catalysis. Molecular dynamics simulation further confirmed the high stability of the three peptide–ACE complexes, with binding free energies from −34.24 to −51.19 kcal/mol. The primary contributing forces include hydrogen bonds, van der Waals interactions, electrostatic forces, and nonpolar solvation effects. Network pharmacology analysis suggested that these peptides may exert synergistic antihypertensive effects by regulating multiple blood pressure-related pathways, including the renin–angiotensin system, renin secretion, and calcium signaling pathways, by acting on key targets such as ACE, REN, SRC, and MMP9. Cell experiments demonstrated that all three peptides exhibited no cytotoxicity in the Ang II-induced HUVEC injury model, significantly promoted NO release, inhibited ET-1 secretion, and possessed endothelial protective potential. This study investigated the in vitro ACE-inhibitory mechanism of peptides derived from camel milk and their potential role in blood pressure regulation, providing experimental evidence for subsequent in vivo activity validation and the development of functional camel milk protein products. Full article

Ferroptosis is a form of regulated cell death driven by iron-dependent phospholipid peroxidation and has emerged as a key mechanism of neuronal injury across a broad spectrum of neurological disorders. MicroRNAs (miRNAs), which function primarily as post-transcriptional regulators of gene expression, are increasingly recognized as important modulators of the regulatory networks governing ferroptosis and as potential therapeutic targets in these conditions. In this review, we synthesize current advances in miRNA-mediated regulation of ferroptosis in neurological disorders. We first outline the core molecular pathways governing ferroptosis, with particular emphasis on antioxidant defense, lipid peroxidation, and iron metabolism. We then integrate evidence from ischemic stroke, intracerebral hemorrhage, epilepsy, toxic encephalopathy, spinal cord injury, Parkinson’s disease, and Alzheimer’s disease, to illustrate how disease-specific miRNA regulatory axes shape ferroptotic vulnerability and its pathological consequences in distinct neurological settings. Importantly, we highlight exosome-based strategies targeting ferroptosis-related miRNA networks as a promising therapeutic approach for neurological disorders, with demonstrated neuroprotective and functional benefits in preclinical studies. Collectively, current evidence supports miRNA-mediated regulation of ferroptosis as an important mechanistic framework and a promising therapeutic target in neurological disorders. Full article

Cadmium (Cd) is a typical heavy metal pollutant in aquatic environments. It enters fish through the gills, digestive tract, and body surface, and accumulates mainly in the liver and kidneys, with species- and tissue-specific distribution. Cadmium triggers apoptosis by inducing oxidative stress, calcium imbalance, and DNA damage. These signals are integrated and amplified by the mitogen-activated protein kinase (MAPK), nuclear factor kappa B (NF-κB), phosphatidylinositol 3-kinase (PI3K)/AKT, and nuclear factor erythroid 2-related factor 2 (Nrf2) pathways, ultimately activating three downstream apoptotic execution pathways: the death receptor, mitochondrial, and endoplasmic reticulum stress pathways. These three pathways form an interactive network through molecular nodes such as BH3 interacting domain death agonist (Bid), Ca²⁺, c-Jun N-terminal kinase (JNK), and C/EBP homologous protein (CHOP), synergistically amplifying the apoptotic effect, with the mitochondrial pathway playing a central role. Cadmium-induced apoptosis is dose-dependent: low concentrations activate protective responses, whereas high concentrations strongly promote apoptosis. Current research gaps remain regarding dynamic pathway crosstalk, chronic low-dose effects, species differences, and fish-specific apoptotic molecules (e.g., caspase-12 homologs). Future studies should focus on constructing multidimensional response maps, clarifying pathway activation thresholds and interaction contributions, and developing composite protective strategies based on Nrf2 activators, metal chelators, and antioxidants, thereby promoting translation into ecological risk assessment and aquaculture pollution control. Full article

Acetylcholine (ACh) is the first identified neurotransmitter and an evolutionarily conserved signaling molecule. Although its role in classical synaptic transmission within the central and peripheral nervous systems has been extensively studied, growing evidence indicates that cholinergic signaling extends beyond neuronal synapses and operates in a broad range of non-neuronal cells. Thus, the cholinergic system represents a complex and widely distributed signaling network with both neuronal and non-neuronal components. Within the nervous system, cholinergic neurons display marked molecular heterogeneity, largely driven by the genomic organization and alternative splicing of the choline acetyltransferase (ChAT) gene. Distinct ChAT mRNA splice variants contribute to region- and cell-type specific cholinergic phenotypes in central and peripheral neurons, including the enteric nervous system, which exemplifies a highly autonomous peripheral cholinergic network. Beyond the nervous system, non-neuronal cholinergic signaling has been identified in epithelial, cardiac, immune, and other cell types, where ACh acts as an autocrine and paracrine regulator of key physiological processes. This review summarizes current knowledge on ACh biosynthesis, focusing on ChAT and its splice variants as molecular determinants of cholinergic diversity and function across neuronal and non-neuronal contexts. Full article

Background: The absence of disease-modifying treatments for Parkinson’s disease (PD)—a neurodegenerative condition with escalating global incidence—represents a critical unmet medical need. Traditionally utilized for both dietary consumption and medicinal preparations, the fruit derived from Rosa roxburghii Tratt demonstrates a remarkably rich profile of biologically active compounds, with flavonoids, triterpenoids, and organic acids representing the predominant classes. Experimental evidence indicates that these compounds elicit robust antioxidative, anti-inflammatory, and neuroprotective effects, making them promising candidates for neurodegenerative disease modulation. This study aimed to systematically evaluate the neuroprotective effects of Rosa roxburghii Tratt juice concentrate powder (RRJCP) across the preventive, interventional, and therapeutic stages of PD and to elucidate its underlying molecular mechanisms. Methods: Rosa roxburghii Tratt juice was subjected to rotary evaporation concentration and vacuum freeze-drying to obtain the juice concentrate powder. C57BL/6 mice were randomly assigned to three main groups (prevention, intervention, and treatment), each containing subgroups including a normal control, an MPTP model group, low-, medium-, and high-dose RRCJP groups (50, 100, and 200 mg/kg), and a positive control Madopar group, totaling 18 subgroups. A chronic MPTP-induced PD mouse model was established. Motor function was assessed via the open field test, pole test, and wire hang test. Substantia nigra neuronal morphology was examined by hematoxylin and eosin staining. The area of tyrosine hydroxylase (TH)-positive regions was measured by immunohistochemistry. The levels of oxidative stress indicators in serum were measured using biochemical kits. Network pharmacology was employed to predict core targets, and the expression of PI3K/AKT pathway and apoptosis-related proteins was determined by Western blotting. Results: Compared with the MPTP model group, RRCJP (200 mg/kg) significantly increased the total distance traveled in the open field, shortened the pole climbing time, and improved the wire hang score. It attenuated the morphological disorganization and nuclear pyknosis of substantia nigra neurons, increased the TH-positive area and TH protein expression, reduced serum MDA content, and elevated the activities of SOD and GSH-Px. Network pharmacology analysis indicated that the PI3K/AKT signaling pathway was among the core targets. Western blotting results further showed that the juice concentrate powder upregulated the expression of p-PI3K, p-AKT, and Bcl-2, while downregulating Bax and Cleaved Caspase-3 levels, which was consistent with the network pharmacology prediction. Conclusions: RRCJP exerts neuroprotective effects across the preventive, interventional, and therapeutic stages in PD model mice, the mechanisms of which may be associated with activation of the PI3K/AKT signaling pathway, attenuation of oxidative stress, and inhibition of neuronal apoptosis. Full article

Artificial intelligence (AI) is increasingly used in cancer research, enabling integrative analysis of complex biomedical data to identify actionable therapeutic vulnerabilities. This review specifically examines how AI advances mechanistic cancer target discovery and translational drug development, focusing on: (1) the processing of large-scale genomics, transcriptomics, proteomics, metabolomics, single-cell profiling, spatial, and clinical datasets using machine learning (ML) and deep learning (DL) algorithms; (2) the identification of candidate biomarkers, driver genes, dysregulated pathways, tumor dependencies, and molecular targets that traditional methods often miss; (3) the integration of multi-omics data, network biology, causal inference, and systems-level modeling to refine mechanistic understanding of cancer progression and separate functional driver events from passengers; and (4) applications in drug development, including virtual screening, molecular modeling, structure-informed target validation, drug repurposing, synthetic lethality prediction, and de novo drug design, which collectively may enhance early-stage drug discovery efficiency. The review underscores that AI serves as both a predictive tool and a platform for linking molecular mechanisms to hypothesis generation, target prioritization, and rational treatment design. Challenges such as data heterogeneity, algorithmic bias, interpretability, reproducibility, regulatory requirements, and patient privacy must be addressed for robust translation and clinical use. Future directions may focus on hybrid approaches that integrate causal modeling, explainable AI, multimodal data, and experimental validation to yield mechanistically grounded, clinically actionable insights. AI-driven approaches ultimately aim to accelerate mechanism-based cancer target discovery and enable more precise, biologically informed anticancer therapies. Full article

Sugars play a pivotal regulatory role in floral bud dormancy release in Prunus mume, a process that critically determines subsequent flowering time. However, the precise molecular mechanisms linking sugar metabolism to this developmental transition remain poorly understood. To address this gap, we integrated physiological profiling and transcriptomic sequencing using two cultivars with contrasting flowering phenologies: the early-flowering ‘Chaotang Gongfen’ (CTGF) and the late-flowering ‘Shichu Jin’ (SCJ). Exogenous sugar treatments were applied separately to floral buds of the cultivar ‘Yilian’ to evaluate the effect of sugars on dormancy release. During dormancy release, glucose and sucrose contents increased progressively and showed significant positive correlations with bud break rates in both CTGF and SCJ (r > 0.75). Consistently, exogenous application of glucose and sucrose significantly accelerated bud break in ‘Yilian’, whereas mannose exhibited an inhibitory effect. Transcriptome analysis of CTGF and SCJ revealed significant enrichment of starch and sucrose metabolism, hormone signal transduction, and stress-responsive pathways. Key metabolic genes, notably the α-amylase gene PmAMY1-2 and the cell wall invertase genes PmCWINV1/4, were upregulated during this transition. Weighted gene co-expression network analysis (WGCNA) further identified PmFRK4, PmSUS6, and the aforementioned invertases as candidate genes within a sugar-associated regulatory module. Collectively, these findings support a model in which glucose and sucrose accumulation promotes endodormancy release via the transcriptional activation of starch and sucrose catabolic pathways. This study provides a theoretical framework for deciphering dormancy regulation in woody perennials and offers potential targets for the precise manipulation of flowering time. Full article

Neuropsychiatric disorders are characterized by complex etiologies, widespread involvement of brain regions, and pronounced clinical heterogeneity, with core pathological mechanisms closely associated with abnormal activity in deep brain structures and their functional networks. Although current pharmacological therapies and conventional neuromodulation techniques have shown therapeutic benefits in certain conditions, they are generally limited by insufficient stimulation depth or the risks associated with invasive procedures. Temporal interference (TI) electrical stimulation has recently emerged as a non-invasive deep neuromodulation technique that generates low-frequency difference-envelope fields through high-frequency carrier signals, thereby enabling relatively precise modulation of deep brain regions while maintaining favorable safety and tolerability. This technique provides a novel technical pathway for precision intervention in neuropsychiatric disorders. In this review, we summarize the principles and technical characteristics of TI stimulation and highlight its recent applications in mood and stress-related disorders, cognitive impairment and neurodegenerative diseases, movement disorders, addiction, and disorders associated with dysregulated neural excitability. We integrate its potential mechanisms across multiple levels, including neural oscillations, deep–cortical network synchronization, reward and motivational circuits, synaptic plasticity and structural remodeling, excitatory-inhibitory balance, and gene and epigenetic regulation. Current evidence suggests that TI stimulation can modulate electrophysiological activity and may engage molecular and network-level processes relevant to functional improvement, although durable clinical benefits remain to be established. Although clinical translation remains challenged by parameter optimization, interindividual variability, and long-term safety evaluation, advances in computational modeling, multimodal neuroimaging, and closed-loop stimulation strategies are expected to facilitate its development. Overall, TI stimulation represents a promising non-invasive deep neuromodulation approach for mechanistic investigation and precision treatment of neuropsychiatric disorders. Full article

Background: Postmenopausal osteoporosis (PMOP) is a common metabolic bone disorder characterized by disrupted bone remodeling due to estrogen deficiency. Erxian Decoction (EXD), a traditional Chinese medicine formula, has shown clinical efficacy against PMOP, but its bioactive constituents and molecular mechanisms remain elusive. Methods: The therapeutic effects of EXD were evaluated in ovariectomized (OVX) mice using micro-CT and bone histomorphometry. Absorbed constituents of EXD were identified by UHPLC-Q analysis. Network pharmacology and quantitative proteomics were integrated to predict the key pathways and targets. The candidate target was validated by in vivo assays, including Western blot, glutathione (GSH) levels, glutathione S-transferases (GSTs) activity, malondialdehyde (MDA), and 4-hydroxynonenal (4-HNE) levels. Molecular docking was performed to assess the binding affinity between bioactive components and the target protein. Results: EXD treatment significantly ameliorated bone microarchitecture deterioration and restored bone remodeling balance in OVX mice. A total of 137 core absorbed constituents of EXD were identified. Integrated network pharmacology and proteomics analyses revealed that EXD primarily modulates the glutathione metabolism pathway to counteract oxidative stress. Glutathione S-transferase A1 (GSTA1) was pinpointed as a potential target. In vivo experiments confirmed that EXD upregulated GSTA1 expression, restored total GSTs activity, replenished GSH reserves, and reduced MDA and 4-HNE levels. Molecular docking demonstrated stable protein–ligand interactions between bioactive components of EXD and GSTA1. Conclusions: EXD alleviates PMOP by activating GSTA1-mediated glutathione metabolism and suppressing oxidative stress. These findings provide a mechanistic basis for the clinical application of EXD in treating PMOP. Full article

Driven by increasing demand in the health and wellness industry, Traditional Chinese Medicine (TCM) agriculture currently faces significant challenges related to supply–demand imbalances and continuous cropping obstacles (CCOs). Intercropping and crop rotation can mitigate yield decline and environmental stress by improving microclimates and rhizosphere ecology. However, there is still a lack of bibliometric synthesis within this research area. To analyze research hotspots and evolutionary trends, 192 articles on the intercropping and crop rotation of medicinal plants were collected from the Web of Science Core Collection (1998–2025), including databases such as the Science Citation Index Expanded (SCIE), the Social Science Citation Index (SSCI) and the Conference Proceedings Citation Index (CPCI). The results revealed a steady increase in publication volume over time. China emerged as the most prolific contributor (93 articles), while the United States occupied a pivotal position in the global collaborative network, achieving a high centrality of 0.90. Research hotspots in this field have evolved from an early emphasis on plant yield and quality toward the mechanisms for alleviating CCOs, interspecific interactions within the rhizosphere microbiome, and the ecological management of soil health. Keyword bursts indicate that “microbial community” and “carbon” have emerged as the current research frontiers. To clarify the micro-mechanisms by which intercropping and crop rotation patterns mitigate or prevent CCOs, future research should prioritize the integration of multi-omics approaches to resolve molecular interactions within the “microbe–plant–soil” nexus. Key priorities include the development of functional Synthetic Microbial Communities (SynComs) and the establishment of comprehensive evaluation systems for ecological cultivation. Furthermore, aligning these models with global climate neutrality strategies would facilitate the balance between high-quality medicinal production and ecosystem stability. Full article