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HomeJournalsCascadia Journal of Biomedical ResearchVolume 16, Issue 310.58302/09sgyf37
Cascadia Journal of Biomedical Research
Review

Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications

Mingdong Liu1, Jiaqi Gong2, Yaqi Liu3, Jiayao Yu2, Zepeng Hu2, Zheng Liu2*

1Department of Orthopaedics, Affiliated Hospital of Shaoxing University, Shaoxing, Zhejiang, China

2Department of Pharmacology, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, China

3Department of Nursing, School of Medicine, Shaoxing University, Shaoxing, Zhejiang, China

* Correspondence: liuzheng1707@163.com

Cascadia J. Biomed. Res. 2024, 16(3), 1719445; https://doi.org/10.58302/09sgyf37

Abstract

The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites—including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules—orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel “metabolite-immune-bone triad” model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.

Keywords:gut microbiotabone diseasescircadian rhythmmulti-omicsmicrobial therapeutics

1 Introduction

As the global population ages, skeletal diseases such as osteoarthritis (OA) and osteoporosis (OP) have emerged as major public health challenges, collectively affecting over 550 million individuals worldwide (1, 2). These disorders are characterized by disrupted bone remodeling dynamics, yet current therapies targeting osteoblast-osteoclast equilibrium remain suboptimal due to incomplete mechanistic insights. Recent advances in the gut-bone axis (GBA) have revealed that gut microbiota-derived metabolites—including short-chain fatty acids (SCFAs), bile acids, and tryptophan derivatives—orchestrate bone homeostasis through immunometabolic crosstalk (3–5). Moreover, an imbalance in the gut microbiota may lead to bacterial and metabolite translocation, which can affect bone health (6–9). Although research in this field is still in its early stages, there is evidence to suggest that modulating the gut microbiota to improve bone health may be a promising therapeutic strategy.

Existing studies predominantly focus on static metabolite-bone interactions, neglecting the dynamic reciprocity between microbial circadian outputs and host bone cells. For instance, although SCFAs exhibit time-dependent effects on osteoclastogenesis, the mechanisms underlying circadian oscillations of G Protein-Coupled Receptor 43 (GPR43) in bone marrow stromal cells—and their disruption in OP—are yet to be elucidated (10). Similarly, bile acid-Farnesoid X Receptor (FXR) signaling shows phase-specific activity in osteoblasts (11), but how microbial metabolite rhythms align with skeletal transcriptional programs remains unknown. These gaps hinder the development of chronotherapeutic strategies targeting the GBA.

To address these challenges, this review underscores the transformative potential of multi-omics integration in elucidating the dynamic crosstalk between gut microbiota-derived metabolites and skeletal health. By leveraging metagenomics, metabolomics, and single-cell RNA sequencing (scRNA-seq), we delineate how microbial metabolites—such as SCFAs, bile acids, and tryptophan derivatives—orchestrate bone remodeling through receptor-mediated signaling (e.g., GPR43, FXR, AhR), epigenetic reprogramming, and immunometabolic regulation. Furthermore, we reveal circadian oscillations in metabolite receptor expression within bone stromal cells, linking microbial diurnal rhythms to osteoblast-osteoclast dynamics. These insights culminate in a novel “metabolite-immune-bone triad” model, which integrates circadian biology with microbiome-driven skeletal regulation. Our synthesis not only resolves prior knowledge gaps regarding temporal host-microbe interactions but also provides a mechanistic foundation for chronotherapeutic and nutritional interventions aimed at treating bone disorders. This work sets the stage for future translational studies, enabling precision medicine approaches that harness microbial metabolites for skeletal disease management.

2 Bone homeostasis and the role of GBA in bone diseases

2.1 Fundamentals of bone homeostasis

The skeleton is a dynamic organ that maintains its strength through continuous remodeling, a process that relies on the delicate balance between bone formation mediated by osteoblasts and bone resorption mediated by osteoclasts. Osteoblasts originate from mesenchymal stem cells, and their differentiation is driven by key signaling pathways such as Wnt/β-catenin and bone morphogenetic proteins; osteoclasts, on the other hand, derive from hematopoietic stem cells, and their formation is centrally regulated by the RANKL/RANK/OPG system. Osteocytes embedded in the bone matrix act as central regulators, coordinating the activities of the aforementioned two types of cells by sensing mechanical signals and secreting factors such as sclerostin (which inhibits the Wnt pathway) and RANKL. Additionally, mesenchymal stem cells in the bone marrow microenvironment compete between osteogenic and adipogenic differentiation pathways, and the tilt of this balance (i.e., the accumulation of bone marrow adipose tissue) is an important mechanism driving bone loss. Finally, systemic hormones such as estrogen play a key role in maintaining bone homeostasis by inhibiting osteoclastogenesis and promoting osteogenesis. Understanding this fundamental framework is crucial for exploring how gut microbiota and their metabolites remotely regulate this complex network through immune, metabolic, and endocrine pathways.

2.2 The role of GBA in bone diseases

Recent advances in microbiology and skeletal disease research have brought increasing attention to the emerging concept of the GBA. This concept delineates a bidirectional communication system wherein gut microbiota influence bone metabolism and health through diverse pathways. Specifically, gut microbes modulate bone density, formation, and resorption. The complex mechanisms underlying the GBA include the production of SCFAs, modulation of the immune system, and direct or indirect effects of gut microbial metabolites on bone cells (5, 12, 13).

OP is a disease characterized by reduced bone density and altered microstructure, which significantly increases the risk of fractures. Studies have shown that gut microbes can regulate bone density by affecting vitamin D synthesis and calcium absorption (5, 8, 14), and SCFAs (such as butyrate and propionate) produced by gut microbes can stimulate the activity of osteoblasts and inhibit the formation of osteoclasts, thereby helping to maintain and enhance bone mass (15–19). However, an imbalance in gut microbes can trigger chronic low-grade inflammation, which is associated with the development of OP (5, 20–22). Inflammatory cytokines such as TNF-α and IL-6 can enhance osteoclast activity, leading to bone loss. Some studies found that modulating the gut microbiota can improve bone density, further confirming the potential regulatory role of gut microbes in OP (23, 24).

OA, characterized by articular cartilage degradation and joint inflammation, may be influenced in its development by gut microbiota through the gut-joint axis. Research indicates that lipopolysaccharides (LPS) derived from gut microbes can induce systemic inflammation, thereby exacerbating joint inflammation and accelerating disease progression (25, 26). Furthermore, alterations in gut microbiota composition can modulate immune responses. For instance, probiotics may alleviate OA symptoms by regulating T-cell activity (5, 27).

The development of bone tumors is intricately linked to chronic inflammation, immune dysregulation, and gut microbiota dysbiosis through GBA. Emerging evidence indicates that gut microbiota-derived metabolites modulate bone tumorigenesis and progression through multiple mechanisms. Dysbiosis-driven systemic inflammation (e.g., elevated circulating LPS) and impaired immune surveillance disrupt bone microenvironment homeostasis, facilitating tumor cell survival and osteolytic activity. Experimental studies demonstrate that gut microbiota depletion reduces bone metastasis burden in murine models, while fecal microbiota transplantation (FMT) from tumor-bearing hosts accelerates osteosarcoma growth, underscoring microbiota’s causal role in bone malignancy (28, 29) (Figure 1).

Diagram comparing health and dysbiosis effects on bone health. Left side shows healthy gut producing SCAFs, activating the GPR43 pathway, leading to osteogenesis and bone health. Right side illustrates dysbiosis causing inflammation, increased TNF-alpha and IL-6, leading to osteoporosis, osteoarthritis, and bone tumors. Arrows indicate the process flow from gut health or dysbiosis to bone conditions.

Figure 1 A panoramic view of the regulatory mechanisms of the microbiota-gut-bone axis in skeletal diseases. Under healthy conditions (left side), short-chain fatty acids (SCFAs, e.g., butyrate/propionate) produced by the gut microbiota activate the GPR43 signaling pathway, directly promoting osteogenesis and inhibiting osteoclastogenesis to maintain bone health. Under gut dysbiosis conditions (right side), decreased SCFA production and microbial imbalance drive skeletal pathogenesis through three distinct pathways: (1) Osteoporosis: Reduced SCFAs and increased pro-inflammatory cytokines (e.g., TNF-α/IL-6) disrupt the bone formation/resorption balance, favoring bone loss; (2) Osteoarthritis: Lipopolysaccharide (LPS) triggers systemic inflammation that spreads to joints, promoting local inflammation and cartilage degradation; (3) Bone Tumor: Dysbiosis impairs immune surveillance (e.g., T cell dysfunction), allowing abnormal cell proliferation and bone tumor formation due to failed elimination. ⊥: Inhibits/decreases.

The gut microbiota modulates bone tumors through three main pathways. First, microbial metabolites such as SCFAs, notably butyrate, exert direct anti-tumor effects by inhibiting histone deacetylases (HDACs) in osteosarcoma cells, promoting cell cycle arrest and apoptosis via p21/WAF1 upregulation. Butyrate also enhances CD8+ T-cell infiltration and polarizes tumor-associated macrophages (TAMs) toward anti-tumor M1 phenotypes via GPR43 signaling (30, 31). Clinically, reduced fecal SCFAs correlate with accelerated bone tumor progression (32, 33). Second, dysbiosis impairs immune surveillance by reducing IL-17A+ γδ T cells and NK cell activity, hindering the elimination of metastatic cells in bone marrow, as shown in germ-free models (34, 35). Tryptophan metabolites (e.g., indole-3-aldehyde) activate the aryl hydrocarbon receptor (AhR) in dendritic cells, boosting anti-tumor CD8+ T-cell responses (36). Third, gut barrier disruption enables pathobiont translocation (e.g., Fusobacterium nucleatum), increasing systemic LPS. This activates TLR4/NF-κB signaling in bone stromal cells, elevating IL-6 and TNF-α, which enhance osteoclastogenesis and form a pre-metastatic niche (37, 38).

3 Role of microbiota metabolite on the cell metabolsim of bone diseases

3.1 Gut microbiota and bone metabolism

The gut microbiota, a complex ecosystem of trillions of microorganisms, significantly influences bone metabolism. Studies demonstrate that probiotics (e.g., Lactobacillus and Bifidobacterium) can enhance bone density (39), while opportunistic pathogens (e.g., Enterobacteriaceae) are linked to bone loss (23). In individuals and models with a conventional gut microbiota, reduced microbial diversity has been observed to correlate with decreased bone density. Notably, the relationship between microbial presence and bone mass is complex and non-linear. Germ-free (GF) mice, which entirely lack microbiota, exhibit a unique skeletal phenotype characterized by suppressed osteoclastogenesis and increased trabecular bone volume compared to conventionally raised mice. This apparent paradox is attributed to the underdeveloped immune system in GF mice, particularly the reduction in osteoclast precursors and pro-osteoclastic immune cells (e.g., CD4+ T cells), leading to diminished bone resorption. This highlights that the complete absence of microbiota creates a distinct immunometabolic state not directly comparable to simply having ‘low diversity’ within a conventional microbiome (23). Additionally, gut microbiota indirectly regulate bone metabolism through immune modulation and inflammatory responses. For example, OP patients exhibit diminished gut microbiota diversity alongside reduced bone density.

A key mechanism involves SCFAs—microbial metabolites derived from dietary fiber fermentation. SCFAs (e.g., acetate, butyrate) mediate bone homeostasis through epigenetic regulation (e.g., histone deacetylase inhibition) and receptor signaling (e.g., GPR activation). Their roles in osteoblast promotion, osteoclast suppression, and circadian synchronization of bone remodeling are detailed in Section 3.2 (14, 17, 40, 41).

3.2 Metabolite signaling pathways in bone homeostasis and diseases

3.2.1 Bidirectional regulation by SCFAs

SCFAs are primary products of gut microbial fiber fermentation. Absorbed via the colon and transported systemically, they serve as energy substrates or signaling molecules. Acetate circulates widely, while propionate is liver-metabolized (17, 42–44). SCFAs exert their effects on bone metabolism through multiple interconnected mechanisms. SCFAs activate GPR41, GPR43, GPR109A and free fatty acid receptors (FFAR2/3), initiating intracellular signaling pathways that regulate hormone secretion, inflammation, and immune function. These receptors exhibit rhythmic expression patterns in bone marrow stromal cells, with GPR43 peaking at midnight, aligning with circadian metabolite flux and suggesting a role for SCFAs in synchronizing bone remodeling through temporal regulation (17, 45). Furthermore, butyrate and propionate drive metabolic reprogramming in osteoclasts by shifting their energy metabolism toward glycolysis and away from oxidative phosphorylation. This metabolic shift downregulates osteoclastogenesis-related genes such as TRAF6 and NFATc1, thereby suppressing bone resorption and enhancing bone density (14, 17). Epigenetically, SCFAs modulate histone acetylation (e.g., H3K27ac) by inhibiting HDACs, influencing osteoblast differentiation and osteoclast activity. For instance, butyrate directly targets TRAF6 and NFATc1 expression to maintain bone homeostasis (40, 41). Advances in multi-omics approaches, including single-cell transcriptomics (scRNA-seq) and metabolomics, have uncovered circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in osteoprogenitor cells. These findings provide a framework for understanding how microbial metabolites like SCFAs synchronize bone remodeling through dynamic interactions between epigenetic modifications (e.g., histone acetylation) and metabolic pathways, as evidenced by temporal alignment of receptor expression and metabolite flux (17) (Figure 2).

Diagram illustrating the interaction between gut microbiota and bone balance. On the left, gut microbiota in the intestine produce acetate, propionate, and butyrate, which are mediated by the GPR43 receptor. The process is shown to influence osteogenesis and osteoclastogenesis, impacting bone homeostasis, inflammation, glycolysis, and oxidative phosphorylation. Below, a graph depicts the cyclical concentration of SCAFs and GPR43 over a 24-hour period, indicated by symbols for day and night.

Figure 2 Circadian regulation of bone metabolism by gut microbiota-derived short-chain fatty acids (SCFAs) via GPR43 signaling. The gut microbiota ferments dietary cellulose to produce SCFAs (acetate, propionate, butyrate), which exhibit diurnal fluctuations in concentration. SCFAs activate the rhythmically expressed GPR43 (G protein-coupled receptor 43) in bone cells, peaking at midnight. This signaling cascade promotes osteogenesis by enhancing the Wnt/β-catenin pathway and suppressing NF-κB-mediated inflammation. Concurrently, SCFAs drive metabolic reprogramming in bone cells, balancing glycolysis and oxidative phosphorylation to favor bone mineralization over resorption. Ultimately, the gut microbiota–SCFA–GPR43 axis orchestrates bone homeostasis through integrated circadian, metabolic, and immune mechanisms. ⊥: Inhibits/decreases.

Although low concentrations of SCFAs (especially butyrate) have been shown to promote osteoblast differentiation and bone formation, in vitro experiments have clearly demonstrated that higher concentrations of butyrate can inhibit the proliferation and differentiation of osteoblasts. The underlying mechanism is related to the induction of cell cycle arrest. For example, studies have indicated that histone deacetylase inhibitors (HDACi) such as butyrate and trichostatin A (TSA), at concentrations that can cause high levels of histone acetylation, will inhibit the expression of osteoblast marker genes (such as Osteocalcin) and matrix mineralization. The mechanism is that HDACi upregulate the expression of the cell cycle-dependent kinase inhibitor p21 Cip1/WAF1, leading to cell cycle arrest of osteoblast precursors in the G1 phase and blocking their differentiation into mature osteoblasts (46). This suggests that the bidirectional regulation of osteoblasts by SCFAs follows the “hormesis” effect (beneficial at low doses, harmful at high doses). Moreover, under specific pathological conditions, SCFAs may exacerbate inflammation and produce complex effects through different immune pathways in specific microenvironments (such as rheumatoid arthritis synovium). For example, studies have shown that SCFAs can promote the differentiation of Th17 cells, which are key subsets of cells that promote inflammation and bone erosion, potentially leading to adverse consequences in autoimmune bone diseases (47).

3.2.2 Bile acid-FXR/Wnt cascade

Bile acids, synthesized by the liver, are essential for the digestion and absorption of lipids and are reabsorbed in the enterohepatic circulation. They also influence bone metabolism through the FXR, which is highly expressed in osteoblasts and plays a significant role in their proliferation (48, 49) FXR, as a major bile acid receptor and a member of the nuclear receptor superfamily, plays a central role in maintaining metabolic homeostasis. It was initially widely recognized for its key roles in regulating bile acid synthesis, lipid metabolism, and glucose homeostasis in the liver and intestine. Upon binding of bile acids to FXR, a series of downstream events are triggered, including the induction of small heterodimer partner (SHP) expression, which in turn inhibits bile acid synthesis and regulates their enterohepatic circulation. In recent years, studies have revealed that FXR also has important functions in bone metabolism. FXR is highly expressed in osteoblasts, and its activation has been shown to directly regulate the expression of osteogenesis-related genes and affect bone energy metabolism, thereby closely linking bile acid signaling to the process of bone formation. Studies have shown that geniposidic acid (GPA) can activate the FXR signaling pathway, upregulating the mRNA expression of osteogenic markers such as Runx2, Osx, and Alpl, increasing the levels of related proteins and Alkaline phosphatase (ALP) enzyme activity, and promoting osteoblast mineralization (50). In an ovariectomized mouse model, GPA was able to increase bone density and quality, enhance bone formation rates, and elevate serum bone formation marker levels, as well as increase the expression of factors such as FXR, SHP, and RUNX2. In FXR gene-knockout mice, the effects of GPA were diminished, confirming that it promotes bone formation through the FXR/RUNX2 signaling pathway, offering a new strategy for the treatment of OP (5, 6, 51, 52).

Furthermore, bile acids enhance osteoblast function through the Wnt/β-catenin signaling pathway, which is crucial for the differentiation of bone marrow mesenchymal stem cells (BM-MSCs), osteoblast formation and function, osteoclast differentiation, and bone resorption. Wnt signaling promotes the differentiation of BM-MSCs into osteoblasts and inhibits adipocyte differentiation, such as Wnt3a activating Transcriptional coactivator with PDZ-binding motif (TAZ) to promote osteogenic differentiation (8, 53). It also enhances osteogenic differentiation and inhibits adipogenic differentiation through the noncanonical JNK pathway. In osteoblasts, Wnt signaling activates Runx2 through β-catenin/TCF1, promoting differentiation and bone formation, while also increasing the expression of bone morphogenetic proteins, which promote osteoblast proliferation and differentiation (54–56). Wnt signaling also inhibits osteoclast differentiation by regulating the expression of RANKL and OPG, such as activating Wnt signaling in osteoblasts to suppress RANKL expression and increase OPG expression, thereby inhibiting bone resorption (57, 58). The activation of the Wnt signaling pathway enhances the sensitivity of osteocytes to mechanical stimuli, promoting bone formation and inhibiting bone resorption. Abnormalities in the Wnt signaling pathway are associated with various bone diseases, such as the inhibition of Wnt signaling leading to bone loss in OP and abnormal activation leading to increased bone mass in osteomalacia (54, 59).The regulation of the Wnt signaling pathway provides new targets for the treatment of bone diseases (57).

Bile acids can inhibit the formation and activity of osteoclasts. For example, chenodeoxycholic acid (CDCA) inhibits osteoclast differentiation through the FXR signaling pathway (48, 60, 61). The mechanism may be related to the upregulation of osteoprotegerin and other osteoclastogenesis inhibitory factors in osteoblasts after FXR activation, thereby indirectly inhibiting osteoclast formation. In addition, studies have shown that the activation of FXR can change the intracellular metabolic environment, but this mainly occurs in osteoblasts and other stromal cells, where it dominates the bone microenvironment by promoting anabolic metabolism, ultimately exerting a net inhibitory effect on osteoclasts (62, 63). In summary, current evidence indicates that bile acids mainly exert an inhibitory effect on osteoclastogenesis in the bone microenvironment through the FXR signaling pathway (Figure 3).

Pathway diagram illustrating the differentiation of bone marrow mesenchymal stem cells (BM-MSCs) into adipocytes or osteogenesis. It involves various signaling pathways including Wnt/β-catenin, JNK, and FXR. The process highlights the role of mRNA, specific proteins like RUNX2 and ALPL, and metabolic processes like glycolysis and oxidative phosphorylation. The image also depicts the influence of bile acids, CDCA, and cholesterol in these pathways, impacting osteoclastogenesis and mineralization. Arrows and blocks indicate activation or inhibition points.

Figure 3 Regulation of bone metabolism by bile acids through FXR and Wnt/β-catenin signaling pathways. Bile acids (e.g., CDCA) and synthetic agonists like GPA activate the Farnesoid X receptor (FXR) pathway. This upregulates the expression of RUNX2/OSX/ALPL, enhancing alkaline phosphatase activity and mineralization. Concurrently, bile acids enhance Wnt/β-catenin signaling via TCF1/TAZ and the non-canonical JNK pathway, further driving BM-MSCs toward osteogenesis and inhibiting adipogenesis. Downstream effects include the inhibition of osteoclastogenesis through metabolic reprogramming (glycolysis, oxidative phosphorylation, and glutamine metabolism). Overall, the FXR and Wnt pathways integrate to coordinate bone formation and resorption.

3.2.3 Tryptophan metabolite-AhR axis

Tryptophan, a precursor to serotonin (5-hydroxytryptamine), melatonin, kynurenine, and niacin, has metabolic byproducts that influence bone remodeling. In diseases of bone metabolism, changes in tryptophan levels occur and play a role in osteoblast differentiation (64) Gut-derived serotonin, which accounts for approximately 95% of the body’s total serotonin, is synthesized by enterochromaffin cells and does not cross the blood-brain barrier. It acts as a potent inhibitor of bone formation. Mechanistically, gut-derived serotonin binds to the 5-HT1B receptor on osteoblasts, inhibiting their proliferation by suppressing cyclic AMP (cAMP) production and cyclin expression. In contrast, brain-derived serotonin, synthesized in the raphe nuclei of the brainstem, functions as a positive regulator of bone mass by enhancing bone formation and reducing bone resorption through a sympathetic nervous system-independent pathway, primarily involving the 5-HT2C receptor in the hypothalamus. The dual origin and opposing actions of serotonin create a complex therapeutic landscape, especially in the context of the widely used selective serotonin reuptake inhibitors (SSRIs). SSRIs increase synaptic serotonin levels to treat depression but also elevate peripheral serotonin bioavailability. Epidemiological studies consistently report that long-term SSRI use is associated with reduced bone mineral density (BMD) and an increased risk of fractures, an effect attributed to the unopposed inhibitory action of gut-derived serotonin on osteoblasts. This presents a clinical dilemma: the neuropsychiatric benefits of SSRIs may come at the cost of skeletal health, particularly in vulnerable populations such as postmenopausal women. Consequently, selectively inhibiting gut-derived serotonin synthesis without affecting the central nervous system has emerged as a promising therapeutic avenue for bone anabolism. Additionally, microbial tryptophan metabolites indole-3-acetic acid (IAA) and indole-3-propionic acid can significantly improve bone loss by repairing intestinal barrier integrity (64–67). These metabolites activate the aryl hydrocarbon receptor (AhR) in the gut, stimulate the Wnt/β-catenin signaling pathway, repair the intestinal barrier, promote osteoblastogenesis, and inhibit osteoclasts. Tryptophan metabolites affect the senescence of musculoskeletal stem cells, with metabolites of the kynurenine pathway such as 3-hydroxykynurenine, kynurenic acid, and anthranilic acid promoting bone aging, reducing bone mineral density, and increasing fracture risk (68). In contrast, 3-hydroxyanthranilic acid, xanthuric acid, picolinic acid, quinolinic acid, and NAD+ increase bone mineral density and reduce fracture risk (69–72) (Figure 4).

Diagram illustrating the tryptophan pathway. Tryptophan converts to serotonin via enterochromaffin cells in the gut and brain, impacting bone formation and resorption. Arrows show interactions with the circulatory system and receptors 5-HT2C and 5-HT1B, linking to processes like bone formation and the cAMP pathway.

Figure 4 Opposing effects of gut- and brain-derived serotonin on bone remodeling. Tryptophan metabolism produces serotonin in two distinct compartments with opposing effects on bone. Gut-derived serotonin (95% of total) acts on osteoblasts via the 5-HT1B receptor, inhibiting bone formation by suppressing cAMP signaling. In contrast, brain-derived serotonin signals through hypothalamic 5-HT2C receptors to promote bone formation and reduce resorption. This duality explains the bone loss associated with drugs that increase peripheral serotonin (e.g., SSRIs), highlighting the gut-derived pathway as a therapeutic target.

3.2.4 Gaseous microbiota-derived metabolites

Emerging evidence indicates that gaseous metabolites derived from gut microbial metabolism of dietary fiber, sulfur-containing amino acids, and proteins—including hydrogen sulfide (H2S), nitric oxide (NO), ammonia (NH3), carbon monoxide (CO), and others—function not as waste products but as signaling molecules that regulate skeletal homeostasis via the gut–bone axis (GBA). Among these, H2S acts as a protective gaseous mediator, similar to NO and CO, and exerts significant effects on nervous, cardiovascular, and skeletal systems, as well as inflammatory processes. It supports skeletal development through antioxidant, anti-inflammatory, and anti-apoptotic mechanisms, notably by rebalancing bone remodeling in OP, stimulating bone formation, and preserving skeletal integrity (73). Please note that CO is different from carbon dioxide and is a gaseous molecule that is often considered toxic due to its high affinity for hemoglobin at high concentrations. However, at low concentrations that are physiologically relevant, it exerts anti-inflammatory and reparative effects via the HO-1 pathway. Meanwhile, gut-derived serotonin, which is regulated by the microbiota, inhibits bone formation when upregulated, illustrating the complex gut-brain-bone crosstalk.

Produced by sulfate-reducing bacteria such as Desulfovibrio spp., H2S promotes osteoblast differentiation via the Wnt/β-catenin pathway and inhibits inflammation-induced osteoclastogenesis through suppression of NF-κB signaling. Studies using the H2S donor sodium hydrosulfide (NaHS) have shown attenuation of dexamethasone (Dex)-induced reactive oxygen species (ROS) generation and ATP depletion, mediated via AMPK pathway activation (74, 75). Furthermore, H2S protects osteoblasts from Dex-induced apoptosis and necrosis through AMPK-dependent mechanisms, highlighting its cytoprotective and antioxidant roles (76). Notably, H2S-releasing compounds have been shown to increase bone mineral density in murine OP models.

NO, generated via microbial nitrite reduction and host eNOS activity, bidirectionally modulates osteoclast–osteoblast coupling through the cGMP–PKG pathway. Bone-implant materials engineered for NO release have demonstrated efficacy in enhancing defect repair. Elevated NH3, produced by proteolytic microbes, aggravates myeloma-related osteolysis by stimulating osteoclast activity, spurring interest in targeting ammoniagenic pathways therapeutically. CO, via the HO-1 pathway, exerts anti-inflammatory and reparative effects, while gut-derived serotonin—under microbiota control—inhibits bone formation when upregulated, illustrating complex gut–brain–bone crosstalk.

Capitalizing on these mechanisms, advanced micro- and nano-delivery systems enabling controlled release of H2S, NO, and CO are being developed. These innovations hold translational promise for preventing implant-related infections, enhancing bone regeneration, and enabling combinatorial gas therapies for complex skeletal disorders (Figure 5).

Illustration of bone remodeling regulation through various pathways. Left: Sources like H2S, nitrite, and protein affect the circulatory and nervous systems. Center: A skeleton representing bone microenvironment. Right: Pathways such as Wnt/β-catenin, cGMP-PKG, and HO-1 influence osteoblast differentiation, osteoclast activity, and inflammation. Balancing osteogenesis and osteoclasts regulates remodeling, prevents osteoporosis, and promotes repair.

Figure 5 Mechanisms of gut microbiota-derived gaseous metabolites in bone remodeling. Gut microbial fermentation produces gaseous metabolites that enter circulation and regulate bone homeostasis. H2S (e.g., from Desulfovibrio) promotes osteogenesis via Wnt/β-catenin signaling and inhibits osteoclastogenesis via NF-κB suppression and AMPK-mediated antioxidant effects. NO bidirectionally modulates osteoclast-osteoblast coupling through the cGMP-PKG pathway. NH3 (from proteolytic bacteria) activates osteoclasts and exacerbates bone resorption. CO exerts anti-inflammatory and pro-repair effects via the HO-1 pathway. These mechanisms inform targeted gas-delivery systems (e.g., nano-scaffolds) for treating bone defects and osteoporosis. Abbreviations: AMPK, AMP-activated protein kinase; HO-1, heme oxygenase-1; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells.↑: Promotes/increases; ↓: Inhibits/decreases.

3.3 Immune regulatory network

3.3.1 Microbiota-immune cell interactions

Modulating the gut microbiota has emerged as a potential therapeutic strategy for rheumatoid arthritis (RA), where probiotics (e.g., Lactobacillus) and prebiotics (e.g., dietary fiber) alleviate RA symptoms and slow disease progression by improving microbial composition (77). For instance, Lactobacillus species prevent bone loss and maintain bone density through modulating the Treg-Th17 cell ratio and inhibiting osteoclastogenesis (78, 79). Additionally, polyphenolic compounds such as ellagic acid exhibit anti-inflammatory effects by regulating the gut microbiota (80, 81). Beyond RA, the gut microbiota critically influences bone remodeling by balancing Th17/Treg dynamics (82). Probiotics (e.g., Lactobacillus reuteri) suppress osteoclast precursor (CD11b+/Gr1-) recruitment and reduce pro-inflammatory cytokines (TNF-α, IL-6) via Treg cell expansion (83, 84). Single-cell immunogenomics further reveal enhanced Th17 infiltration and metabolic reprogramming of GPR43+ macrophages in osteoporotic bone marrow, highlighting microbial metabolites’ role in mediating “metabolite-immune dialogue” to regulate the bone microenvironment (85).

3.3.2 Bone loss mediated by inflammatory cytokines

Microbial products such as LPS induce chronic low-grade inflammation and promote RANKL-dependent osteoclastogenesis through the TLR4/NF-κB pathway (86, 87). Clinical cohort data show that serum TNF-α levels in OA patients are negatively correlated with gut microbiota diversity (88). Mechanistically, SCFAs produced by gut microbiota can reduce NLRP3 inflammasome activation by inhibiting histone deacetylase 6 (HDAC6), thereby attenuating inflammatory responses (89, 90). Additionally, FMT therapy has been shown to reduce IL-1β levels in a randomized controlled trial (RCT), verifying the clinical translational potential of the “immune-bone axis.” These findings highlight the critical role of the gut microbiota in modulating systemic inflammation and its impact on bone health, suggesting that microbiota-targeted therapies may have therapeutic potential for inflammatory bone diseases (49, 90–92).

3.3.3 Microbiota-immune clock synergy

Disruption of circadian rhythms alters the structure and function of the gut microbiota, impacting host metabolism and immune function (93–95). Microbial metabolites (e.g., SCFAs) regulate host immune cell function and infiltration by activating receptors (e.g., GPR43) (96, 97) and modulate gene expression via epigenetic mechanisms like histone modifications (96, 98). These actions affect bone matrix cells, thereby regulating bone metabolism (18, 99, 100). Concurrently, circadian rhythms directly regulate immune cell function; their disruption impairs intestinal immune barrier function, increasing sensitivity to endotoxins like LPS (101–103). Therefore, the gut microbiota, through its metabolic signaling and in coordination with the host’s immune circadian rhythms, constitutes the “metabolite-immune-bone triad model” to maintain bone homeostasis (5, 49, 104).

Experimental validation of the “metabolite-immune-bone triad” in animal models provides mechanistic credibility to this integrative framework: Probiotic-mediated Treg expansion ameliorates bone loss in ovariectomized (Ovx) mice, where Lactobacillus reuteri supplementation increased bone marrow Treg frequency by 2.1-fold, suppressed osteoclast precursor recruitment, and reduced trabecular bone loss by 32% compared to controls. This correlated with decreased serum TNF-α and IL-6 levels, confirming microbiota-immune crosstalk in skeletal protection. Germ-free (GF) mouse studies reveal direct immune-bone coupling: GF mice exhibit 40% higher trabecular bone volume alongside reduced CD4+T cells and osteoclast precursors (CD11b+/Gr1-) in bone marrow.Reconstitution with conventional microbiota normalized immune cell profiles and decreasing the bone mass to normal levels. SCFAs synchronize circadian bone remodeling through epigenetic-immune coordination. Butyrate gavage in mice elevated H3K27ac acetylation at GPR43 promoter regions in bone stromal cells, amplifying midnight receptor expression by 3.5-fold. This enhanced Treg differentiation and suppressed NLRP3 inflammasome activation, reducing osteoclastogenesis by 45% in circadian-misaligned models.These findings solidify the triad model: microbial metabolites (e.g., SCFAs) rhythmically engage immune cells (Treg/Th17) and epigenetic machinery (H3K27ac) to orchestrate bone remodeling, offering actionable targets for chronotherapeutic interventions.

3.4 Therapeutic implications: translating mechanistic insights into interventions

The comprehensive mechanistic studies reviewed above reveal that gut microbiota-derived metabolites (SCFAs, bile acids, tryptophan derivatives, and H2S) precisely regulate bone homeostasis through multidimensional pathways: receptor signaling (e.g., GPR43, FXR, AhR), epigenetic reprogramming (HDAC inhibition/H3K27ac acetylation), metabolic remodeling (glycolysis-oxidative phosphorylation balance), immune modulation (Th17/Treg balance, inflammatory cytokine inhibition), and circadian coordination (receptor oscillatory expression). These findings lay a direct theoretical foundation and provide actionable targets for developing precision therapies targeting the gut-bone axis:

SCFAs pathway inhibits osteoclast differentiation and promotes osteoblast metabolic reprogramming through GPR43/HDAC signaling, directly supporting the use of SCFA-producing probiotics (such as Lactobacillus reuteri) and dietary fiber interventions, and providing a basis for developing GPR43 agonists or selective HDAC6 inhibitors (18); the circadian oscillation of its receptor further drives the clinical translation of chrono-nutritional strategies (such as timed fiber supplementation) (15). The bile acid/FXR/RUNX2-Wnt cascade validates the pharmacological effects of FXR agonists (such as geniposide) and microbiota-modulating agents on bone formation, opening up new avenues for OP drug development (11). The tryptophan metabolite-AhR axis promotes bone formation by repairing the intestinal barrier and activating the Wnt signal, supporting the application of AhR ligands, tryptophan-metabolizing probiotics, or functional nutrients to synergistically inhibit NLRP3 inflammasome activation (64). The bone-protective effects of H2S suggest that H2S donors (such as sodium hydrosulfide) or H2S-producing microbial transplantation may reduce oxidative stress damage in osteoblasts (105).

The regulation of the immune-metabolic network provides scientific support for probiotics, FMT, and cytokine-targeted therapies (such as anti-TNF-α biologics) to reshape the Th17/Treg balance and inhibit inflammatory bone loss. Especially crucial is the “metabolite-immune-circadian” triad model, which integrates circadian rhythms into therapeutic design and advocates for time-resolved intervention strategies based on host-microbe metabolic rhythms. The precise correspondence between these mechanistic targets and therapeutic approaches marks a substantive leap from basic discovery to clinical translation—offering a new paradigm for precision microbiota-based therapies for OP, OA, and other related diseases (Table 1).

Table 1 Key mechanisms, effects, and therapeutic strategies of gut microbiota-derived metabolites in skeletal disorders.

MetabolitesSignaling pathwayKey function/mechanismEffects on bone cellsDirection of effectRelated diseasesIntervention strategiesRef.
SCFAsGPR43/FFAR2; HDAC inhibition↓ osteoclastogenesis; promote osteoblast glycolysis shift; epigenetic modulation (e.g., H3K27ac); circadian synchronization↓ osteoclastogenesis; promote osteoblast function→OP, OASCFA-producing probiotics (e.g., L. reuteri); dietary fiber; GPR43 agonists; HDAC6 inhibitors(14, 17, 18, 40, 41)
Bile AcidsFXR; Wnt/β-catenin↑ osteoblast differentiation and mineralization via RUNX2/Osx; ↓osteoclastogenesis; ↑ bone formation↑ osteogenesis; ↓ osteoclast differentiation→OP, OAFXR agonists (e.g., geniposidic acid - GPA); microbiota-modulating agents(5, 48, 50, 51)
Tryptophan DerivativesAhR; Wnt/β-cateninRepair intestinal barrier; inhibit NLRP3 inflammasome; promote osteoblastogenesis; regulate osteoimmunity↑ osteogenesis; ↓ osteoclasts→Inflammatory bone loss, OPAhR ligands; tryptophan-metabolizing probiotics; functional nutrients(64, 65)
Gut-derived
Serotonin		–↓ bone formation↓ osteoblast proliferation←OP–(106, 107)
Brain-derivedSerotonin–↑ bone formation and inhibit bone resorption↑ osteoblast activity; ↓ osteoclastogenesis→OP–(106, 107)
Melatonin–↑ osteoblast differentiation; anabolic and anti-resorptive effects↑ osteogenesis;
↓ resorption		→OP–(3, 108)
Kynurenine Pathway–↓ BMSC proliferation and osteoblast differentiation; promote bone aging↓ bone formation←OP–(68, 69, 109)
Tryptophan Metabolites (IAA, IPA)AhR; Wnt/β-cateninRepair intestinal barrier; activate AHR; stimulate Wnt/β-catenin; promote osteogenesisPromote osteogenesis; improve bone density→OPProbiotics; tryptophan supplementation(64–67)
H2SWnt/β-catenin; NF-κB; AMPKAntioxidant; anti-apoptotic; ↑ osteoblast differentiation; inhibits inflammation-induced osteoclastogenesis↑ osteogenesis; ↓ osteoclastogenesis→OP, OAH2S donors (e.g., NaHS); transplantation of H2S-producing bacteria (e.g., Desulfovibrio)(73–75, 105)
NOcGMP-PKG pathwayRegulation of osteoclast-osteoblast coupling;
↑ bone defect repair		Bidirectional regulation↔Bone defects, OPNO-releasing bone implant materials(3, 73)
COHO-1 pathwayAnti-inflammatory; ↑ bone repair↑ bone repair→BII, osteonecrosisTargeting HO-1 pathway(73)
NH3–↑ osteoclast activity; aggravates osteolysis↑ osteoclast activity←Multiple myelomaTargeting ammoniagenic bacteria(73)
Immune-
Metabolic Network		Th17/Treg; TNF-α,IL-1β; RANKL/OPGModulate systemic inflammation; regulate osteoclastogenesis; maintain bone-immune homeostasisModulate bone remodelingVariableOP, OA, RAProbiotics; Prebiotics; FMT; Anti-cytokine biologics (e.g., anti-TNF-α, anti-IL-1β)(49, 82–84, 87)
Circadian IntegrationGPR43, FXR; H3K27acSynchronize osteoblast-osteoclast dynamics through epigenetic-immune coordination; temporal regulation of bone remodelingSynchronize bone remodeling→OP, OAChronotherapeutic interventions; time-based probiotic/fiber dosing(10, 17, 24)

↑, Promotes/increases; ↓, Inhibits/decreases; →, Positive; ←, Negative ↔, Bidirectional; AhR, Aryl Hydrocarbon Receptor; AMPK, AMP-activated Protein Kinase; BII, Bone implant infection;CO, Carbon Monoxide;FMT, Fecal Microbiota Transplantation; FXR, Farnesoid X Receptor; GPA, Geniposidic Acid; GPR, G Protein-Coupled Receptor; GPR43, G Protein-Coupled Receptor 43; HDAC, Histone Deacetylase; HO-1, Heme Oxygenase-1; H2S, Hydrogen Sulfide; IAA, Indole-3-Acetic Acid; IL, Interleukin; IPA, Indole-3-Propionic Acid; NaHS, Sodium Hydrosulfide; NF-κB, Nuclear Factor Kappa-Light-Chain-Enhancer of Activated B Cells; NH3, Ammonia; NLRP3, NLR Family Pyrin Domain Containing 3; NO, Nitric Oxide; OA, Osteoarthritis; OP, Osteoporosis; OPG, Osteoprotegerin; RA, Rheumatoid Arthritis; RANKL, Receptor Activator of Nuclear Factor Kappa-B Ligand; RUNX2, Runt-Related Transcription Factor 2; SCFAs, Short-Chain Fatty Acids; TNF-α, Tumor Necrosis Factor Alpha; Treg, Regulatory T Cell; Wnt, Wingless-related Integration Site.

3.5 Metabolite-bone temporal dynamics

The circadian oscillations of gut microbiota metabolites are a key bridge connecting the host circadian clock with bone metabolism. The production of SCFAs peaks during the active phase, in sync with the host’s feeding patterns. Studies have shown that the concentrations of acetate, propionate, and butyrate in the cecum of mice are 30-50% higher during the dark (active) phase than during the light phase (115). This rhythmic variation directly regulates the diurnal fluctuations of bone metabolism: SCFAs inhibit osteoclast differentiation at night through GPR43 signaling, while bile acids promote osteoblast differentiation during the day via FXR signaling, forming a complementary temporal coordination (48). The specific mechanisms involve multi-level spatiotemporal control: time-restricted feeding can enhance the circadian amplitude of SCFAs and improve bone density. In mouse models, restricting the feeding window to 12 hours within the active phase can increase bone formation rates by 25% (115). The circadian rhythm of glucocorticoids regulates the temporal distribution of metabolites by modulating gut permeability and microbial composition. The morning peak of cortisol can enhance SCFA production, indirectly promoting daytime bone formation (14, 95, 116). Individual circadian pattern variations significantly impact the function of the gut-bone axis. Polymorphisms in the PER3 gene lead to differences in “morningness” and “eveningness” chronotypes, affecting the phase of metabolite rhythms. Individuals carrying the long allele of PER3 have a 2–3 hour phase advance in SCFA rhythms, which may explain their differential susceptibility to shift work-related bone loss (117, 118). Age-related attenuation of rhythmic amplitude also leads to flattened metabolite oscillations in the elderly, which is associated with an increased risk of osteoporosis (62, 119).

4 Biomarkers in the gut-bone axis: implications for pathogenesis and clinical management

GBA represents a dynamic, bidirectional communication network between the gastrointestinal and skeletal systems, orchestrated through immune, metabolic, and microbiome-derived signaling pathways. Inflammatory biomarkers such as TNF-α and IL-6 play pivotal roles in promoting osteoclastogenesis via RANKL/NF-κB activation in inflammatory conditions like inflammatory bowel disease (IBD) and rheumatoid arthritis, while C-reactive protein (CRP) levels are inversely correlated with bone mineral density (87, 110). Meanwhile, bone turnover markers—including β-CTX (reflecting osteoclast activity) and PINP/osteocalcin (indicating osteoblast function)—are frequently dysregulated in metabolic bone diseases. Notably, gut microbiota influence osteocalcin’s γ-carboxylation, further linking microbial ecology to bone metabolism (111, 112). Together, these biomarkers facilitate early detection of inflammatory bone loss and allow for monitoring therapeutic responses to biological agents such as anti-TNF-α antibodies.

Gut microbiota-derived metabolites are central regulators of bone homeostasis. SCFAs exert osteoprotective effects by promoting regulatory T cell (Treg) differentiation and inhibiting osteoclastogenesis, whereas lipopolysaccharide (LPS) exacerbates bone resorption through TLR4/NF-κB signaling (113). These mechanisms are exemplified in germ-free mice, which exhibit elevated bone mass accompanied by reduced osteoclast precursors (CD11b+/Gr1-), lowered TNF-α and IL-1 expression, and altered serotonin metabolism due to suppressed Tph1 activity (120, 121). Additionally, hormonal regulators—including vitamin D (25(OH)D3), parathyroid hormone (PTH), and fibroblast growth factor 23 (FGF23)—modulate bone mineralization. Deficiencies in these factors often lead to secondary hyperparathyroidism and accelerated bone loss, particularly in malabsorption syndromes.

In OA, the bone-cartilage interface offers critical biomarker insights: CTX-II levels correlate with osteophyte formation (122, 123),and IL-1β drives cross-tissue degradation via matrix metalloproteinase activation (124). Proteomic studies further indicate dysregulation of subchondral bone during early OA, though these findings await broader validation. The RANKL/OPG ratio and zonulin—a marker of intestinal permeability—provide additional mechanistic insight, with elevated RANKL observed in postmenopausal osteoporosis and zonulin predicting bone loss associated with microbial translocation (114). Collectively, these findings support the use of combined biomarker panels incorporating gut-immune signals (e.g., serotonin, TNF-α) and osteochondral markers (e.g., CTX-II, IL-1β) for a more comprehensive assessment of bone health.

Clinically, integration of GBA biomarkers enables mechanistic stratification of bone disorders (e.g., inflammatory vs. metabolic origins) and guides personalized interventions such as microbiome modulation, nutritional support, and targeted biologics like anti-IL-1β agents in OA (125, 126). Future multi-omics approaches—including metagenomics and metabolomics—promise to unveil novel biomarkers, advancing precision medicine for osteoporosis, inflammatory osteopathies, and age-related skeletal decline. This integrative framework not only aids early risk detection in high-risk populations such as IBD patients but also enables monitoring of OA progression through osteochondral markers and supports the development of novel therapies targeting gut-microbiota-bone signaling pathways.

Recent single-cell transcriptomic studies have revealed circadian oscillations in metabolite receptors (e.g., GPR43, FXR) within bone marrow stromal cells. Disruption of these rhythms in osteoporosis patients underscores a “metabolite-immune clock” model, wherein microbial metabolites help synchronize osteoblast-osteoclast dynamics through epigenetic mechanisms such as H3K27ac acetylation (114) (Table 2) (142).

Table 2 Biomarkers of bone diseases in the gut-bone axis.

CategoryMarkerFunctionKey mechanismRelated diseasesRefs.
InflammationTNF-αPro-inflammatory; ↓OB; ↑OCActivates NF-κB; ↑RANKLRA, IBD, OP(5, 20, 21, 87)
IL-6↑Osteoclastogenesis; ↓bone formationActivates JAK/STATIBD, postmenopausal OP(5, 20, 21, 87)
IL-17↑Bone resorption; ↓bone formationStimulates RANKL secretionAS, PsA(88)
CRPSystemic inflammation marker; ↓BMDNegatively correlates with BMDChronic bone loss(87, 110)
Bone Metabolismβ-CTXBone resorption markerCollagen breakdown, OC activity↑OP, Paget’s disease(111)
PINPBone formation markerCollagen synthesis, OB activity ↑OP, osteomalacia(111)
OCRegulates mineralization; bone formationSecreted by osteoblasts; reflects bone formation; Gut microbiota modulates γ-carboxylationOP, fracture risk(111, 112)
TRAP-5bOC-specific enzyme; bone resorption↑Acid phosphatase activityMultiple myeloma, OP(111)
Gut
Microbiota		SCFAsAnti-inflammatory; ↓OC; ↑bone formationActivate GPR43/41; ↑Treg differentiationIBD, OP(14, 17, 18, 113)
LPSPro-inflammatory; ↑bone resorptionActivates TLR4/NF-κB; ↑RANKLMetabolic bone disease(25, 26, 37, 86)
Vitamins/
Hormones		25(OH)D3↑ Ca²+ absorption; bone mineralizationDeficiency → secondary hyperparathyroidismRickets, OP(5, 8, 14)
PTHRegulates Ca²+/P metabolism; ↑bone resorption↑OC activation in hypocalcemia/VitD deficiencySecondary OP,
renal osteodystrophy		(5)
FGF23↓Phosphate reabsorption; modulates VitDGut dysbiosis may alter expressionCKD-MBD(5)
Other
Molecules		RANKL/OPGRANKL: ↑OC; OPG: inhibitorGut inflammation ↑RANKL; disrupts balancePostmenopausal OP, RA(57, 58, 114)
ZonulinGut permeability markerBarrier breach → LPS translocation → bone lossCD, IBD-related OP(9, 114)
IgAGut immune regulationMucosal immunity disruption
effects bone metabolism		Autoimmune bone disorders(5, 49)

↑, Promotes/increases; ↓, Inhibits/decreases; AS, Ankylosing Spondylitis; BMD, Bone Mineral Density; CKD-MBD, Chronic Kidney Disease-Mineral and Bone Disorder; CD, Celiac disease; CRP, C-Reactive Protein; FGF23, Fibroblast Growth Factor 23; GPR, G Protein-Coupled Receptor; IBD, Inflammatory Bowel Disease; IgA, Immunoglobulin A; IL, Interleukin; LPS, Lipopolysaccharide; NF-κB, Nuclear Factor Kappa-Light-Chain-Enhancer of Activated B Cells; OB, Osteoblast; OC, Osteocalcin; OP, Osteoporosis; OPG, Osteoprotegerin; PINP, Procollagen Type I N-Terminal Propeptide; PsA, Psoriatic Arthritis; PTH, Parathyroid Hormone; RA, Rheumatoid Arthritis; RANKL, Receptor Activator of Nuclear Factor Kappa-B Ligand; SCFAs, Short-Chain Fatty Acids; TLR4, Toll-Like Receptor 4; TNF-α, Tumor Necrosis Factor Alpha; TRAP-5b, Tartrate-Resistant Acid Phosphatase 5b; Treg, Regulatory T Cell; VitD, Vitamin D.

5 Clinical interventions of bone disorders based-GBA

5.1 Dietary interventions

The gut microbiota significantly influences bone health through nutrient-mediated mechanisms, particularly by enhancing monosaccharide absorption and energy harvesting (5, 23, 140, 143). Specific strains, such as Lactobacillus plantarum, have been shown to stimulate skeletal development under malnutrition conditions, suggesting that microbiota modulation could optimize nutrient utilization for bone health enhancement. Dietary fiber bridges gut microbiota and bone health through microbial fermentation-derived SCFAs. This process not only acidifies the intestinal environment but also generates SCFAs that reinforce gut barrier integrity and suppress systemic inflammation, thereby indirectly supporting skeletal homeostasis (127, 128). Increased dietary fiber intake positively modulates microbial composition, establishing a beneficial dietary-microbiota-bone axis (144, 145).

5.2 Prebiotics

Prebiotics, including inulin and fructooligosaccharides (FOS/GOS), augment mineral bioavailability through gut microbiota remodeling. Fermentation of these fibers elevates SCFAs production, which acidifies intestinal pH to enhance calcium solubility and activates mineral transport pathways (129). Clinical trials demonstrate that daily intake of 8 g inulin-type fructans increases calcium absorption by 12% in adolescents and improves whole-body bone mineral density within one year, paralleled by Bifidobacterium enrichment (129, 130). Similarly, soluble corn fiber enhances calcium retention in postmenopausal women dose-dependently, correlating with increased Lachnospiraceae and Bacteroides abundance (130). Mechanistically, prebiotics reshape microbial composition (e.g., reduced Firmicutes/Bacteroidetes ratio) and modulate metabolic pathways for carbohydrate/lipid utilization, synergistically promoting calcium absorption and bone mechanical strength (130). These effects are further amplified by SCFA-mediated expansion of intestinal absorptive surface and permeability (130, 146). Collectively, prebiotic-driven microbiota modulation offers a dietary strategy to combat OP, particularly in calcium-deficient populations (129).

5.3 Probiotics

Probiotics demonstrate osteoprotective effects through microbiota-immune interactions. Lactobacillus reuteri enhances bone density in healthy male mice by suppressing intestinal inflammation and restructures gut microbial communities in ovariectomy (Ovx) models, effectively attenuating estrogen deficiency-induced bone loss (131, 147). Mechanistically, L. reuteri inhibits osteoclastogenesis via dual pathways: downregulating bone marrow CD4+ T cell recruitment (key osteoclast activators) and directly suppressing osteoclast differentiation in vitro. These actions correlate with reduced bone resorption markers and preserved trabecular architecture (131, 148). Similarly, L. paracasei and L. plantarum mitigate hormone deficiency-driven OP, highlighting genus-specific modulation of bone remodeling pathways (130, 148–150).

5.4 FMT

The efficacy of FMT in treating OP exhibits considerable heterogeneity, influenced by factors including donor selection (e.g., potential fecal pathogens affecting safety) (137, 138), recipient response, host gut microbiota composition/function, donor microbial diversity, immune status, and administration protocols (151, 152). Variations in donor microbiota, host immunity, and delivery methods further contribute to inconsistent outcomes (153). The composition and function of the donor microbiota are the “cornerstones” determining the success of FMT. The concept of “super donors” suggests that certain donors’ microbiota have higher engraftment capabilities and stability. For example, the presence of Akkermansia muciniphila (which improves gut barrier function) (154), Faecalibacterium prausnitzii (anti-inflammatory) (155), and high SCFA-producing Lachnospiraceae and Ruminococcaceae in the donor microbiota are associated with better osteoprotective effects (23). Conversely, if potential pathogens (such as Enterobacteriaceae) in the donor microbiota are not adequately screened, it may lead to FMT failure or even exacerbate bone loss. Additionally, the recipient’s intrinsic environment serves as the “soil” for microbial engraftment, and its condition is crucial. The recipient’s low microbial diversity, high proportion of antibiotic-resistant bacteria, or specific microbial structure can resist the implantation of new microbiota, a phenomenon known as “colonization resistance.” For instance, a high abundance of Bacteroides in the recipient’s gut may hinder the engraftment of other strains. The host’s immune status (such as Treg/Th17 balance), genetic background (such as polymorphisms in immune-related genes), and gut barrier integrity together form a unique microenvironment that determines the fate of the transplanted microbiota and the variability of immune modulation effects (156). Moreover, the type and preparation of the FMT formulation also affect the efficacy. Different methods, such as fresh versus frozen fecal preparations and oral capsules versus endoscopic infusion, have significant impacts on microbial viability and delivery efficiency. The freeze-thaw process may damage the viability of some strictly anaerobic bacteria, while the enteric coating technology of capsules affects the precise release of microbiota in the gut.

FMT restores gut microbiota diversity and shows osteoprotective effects in preclinical models. In ovariectomy-induced OP, FMT inhibits osteoclastogenesis and improves bone density via microbiota-metabolite interactions; in OA, it reduces inflammation through Th17/Treg modulation (52, 132). Clinical data indicate immunomodulatory shifts in IBD patients after FMT, suggesting bone benefits via the gut-bone axis (149, 157). Mechanisms include enrichment of anti-inflammatory taxa, regulation of bone remodeling via microbial metabolites (e.g., SCFAs), and modulation of osteoclast-related cytokines (149, 158).

Future directions involve elucidating microbiota-bone crosstalk, validating efficacy via RCTs, and exploring combination therapies with nutritional or pharmacological interventions. Preventive FMT applications in high-risk populations warrant further investigation (Supplementary Table 1).

5.5 Traditional Chinese medicine

TCM represents a holistic medical system with a history spanning thousands of years. For the purpose of this review, which focuses on the GBA and metabolic regulation, we specifically refer to the phytochemical or herbal medicine component of TCM, rather than practices such as acupuncture or Tai Chi. Numerous active compounds derived from TCM herbs have demonstrated potent osteogenic, angiogenic, and anti-inflammatory properties in preclinical studies, positioning them as promising candidates for bone tissue engineering and the management of metabolic bone diseases. Among the most extensively studied osteo-promotive TCM compounds are flavonoids (e.g., icariin and icaritin) (159), polyphenols (e.g., resveratrol) (160, 161). To enhance clarity for a global readership, we will elucidate the botanical origins and mechanisms of these specific compounds:

Icariin and Icaritin: These are prenylated flavonoids isolated from the herb Epimedium (commonly known as Horny Goat Weed). They are recognized as principal active constituents responsible for the bone-strengthening effects traditionally attributed to Epimedium in TCM theory. Mechanistically, icariin and icaritin significantly enhance the proliferation and differentiation of osteoblasts by upregulating key osteogenic genes, including RUNX2, ALP, Osteocalcin (OCN), and Collagen I (COLI) (159, 162). Furthermore, they promote intraosseous angiogenesis—a critical process for bone regeneration—via the VEGF and HIF-1α pathways (56, 133–136, 139, 141, 163–168).

Resveratrol: While also present in grapes and berries, resveratrol is a stilbenoid polyphenol abundantly found in Polygonum cuspidatum (Japanese Knotweed), a plant used in TCM. Similar to baicalin, resveratrol exhibits strong anti-inflammatory and antioxidant effects (160, 161). It helps protect bone cells from oxidative damage and suppresses pro-inflammatory pathways, thereby preserving bone mass and promoting a healthy remodeling balance.

Additionally, TCM components like baicalin and resveratrol exhibit potent anti-inflammatory and antioxidant effects, mitigating oxidative stress and creating a favorable microenvironment for bone regeneration (136, 167–169).

While the direct modulation of the microbiota-GBA by TCM remains underexplored, its systemic effects on bone metabolism and inflammation suggest potential interactions with gut microbiota. For example, TCM may enhance gut barrier function and reduce systemic inflammation by modulating microbial composition and metabolite production, such as SCFAs and bile acids, thereby indirectly supporting bone health (167, 170). Future research should focus on elucidating these mechanisms to optimize TCM-based strategies for bone regeneration and disease management (Figure 6) (Table 3).

Illustration showing the effects of different dietary and treatment approaches on gut and bone health. High-fiber foods and prebiotics increase short-chain fatty acids (SCFAs), enhancing calcium absorption and bone mineralization. Probiotics inhibit pathogenic bacteria, influencing T cell activity and reducing bone resorption. Fecal microbiota transplantation (FMT) restores beneficial bacteria, impacting inflammation and bone connectivity. Traditional Chinese Medicine (TCM) affects pathways related to inflammation and oxidative stress, supporting osteogenesis and inhibiting osteoclastogenesis.

Figure 6 Five-pronged therapeutic strategies targeting the gut-bone axis to restore skeletal homeostasis. ① High-fiber diets yield microbiota-derived short-chain fatty acids (SCFAs) that activate G Protein-Coupled Receptor (GPR)41/43, enhancing calcium absorption and osteogenesis while suppressing osteoclastogenesis. ② Prebiotics (e.g., inulin) amplify SCFA production, promoting intestinal epithelial proliferation to increase absorptive surface area and expand beneficial bacteria.③ Probiotics (e.g., Lactobacillus) directly inhibit pathogenic bacteria, reduce pro-inflammatory cytokines (TNF-α/IL-6), and block RANKL-NFATc1 signaling to limit T-cell migration to bone marrow and bone resorption. ④ Fecal microbiota transplantation (FMT) restores microbial balance by elevating beneficial taxa and suppressing harmful bacteria, augmenting Treg cells to resolve inflammation-driven bone loss. ⑤ Traditional Chinese Medicine (TCM) activates the Wnt/β-catenin pathway and VEGF-mediated intra-bone angiogenesis to stimulate osteogenesis, while inhibiting NF-κB and reactive oxygen species (ROS) to mitigate oxidative stress and resorption. These interventions collectively remodel the bone microenvironment through immunometabolic crosstalk.↑: Promotes/increases; ⊥: Inhibits/decreases.

Table 3 Systematic comparison of clinical interventions based on the gut-bone axis.

CategoryDietary interventionsProbioticsPrebioticsFMTTCMRefs.
Mechanism of ActionBoost gut barrier; ↓inflammationModulate microbiota; ↓osteoclast differentiation↑SCFAs; ↑Ca2+ absorptionRestore microbiota balance; ↓LPS/TLR4 → ↓inflammationMulti-target (e.g., Icariin→Wnt/β-catenin); Antioxidant(52, 78, 79, 127–136)
Clinical Efficacy12%↑BMD (teens, inulin); 12%↑Ca2+ absorption5–10%↑BMD (postmenopausal); 25%↓IL-68%↑BMD (postmenopausal, inulin); 15%↑Ca2+ retention15%↑BMD (OVX mice); 32%↓TNF-α (RCT)8–12%↑BMD; 20%↑osteocalcin(52, 84, 129–132, 135, 136)
Type of Study and Level of EvidenceRCT (B)RCT Phase II (B)RCT + Animal (B)Animal + RCT Phase II (B)Meta-analysis + Cellular (C)(52, 84, 129, 130, 132) (135, 136)
AdvantagesSafe, low cost, good adherenceStrain-specific efficacy; combinableBroad applicability (no live bacteria)Potent (refractory cases); holisticMulti-component synergy;
high acceptance		(52, 78, 127, 129, 131–134)
LimitationsSlow effect, limited in severe casesStrain variability; unstable long-term effectsHigh dose → GI discomfortUnknown long-term safety; donor screeningComplex composition;
lack of RCTs		(127, 130, 131, 137–139)
Target PopulationAdolescents/poor Ca2+ absorption; early OP preventionPostmenopausal women; mild OPElderly/inadequate Ca2+ intake; high-risk OPSevere OP; arthritis w/bone destructionChronic bone diseases; natural therapy preference(52, 84, 129, 130, 132, 135, 136)
Ethics and ComplianceNo ethics approval; low privacy riskGRAS; strain safety assessmentGRAS; dose standardizationIRB approval; donor anonymization (GDPR)Minimal ethical issues; GMP required(78, 127, 129, 137, 139)
Future Research DirectionsPersonalized diets; long-term BMD trackingStrain-metabolite combos; dose optimizationNew prebiotic screening; multi-population validationFreeze-dried capsules; 10-yr safety follow-upMonomer mechanism (e.g., icariin); multicenter RCTs(131, 135, 137, 140, 141)

↑, Increase/improvement; ↓, Decrease/reduction; BMD, Bone Mineral Density; Ca, Calcium; FMT, Fecal Microbiota Transplantation; GDPR, General Data Protection Regulation; GI, Gastrointestinal; GMP, Good Manufacturing Practice; GRAS, Generally Recognized As Safe; IRB, Institutional Review Board; OP, Osteoporosis; OVX, Ovariectomized; RCT, Randomized Controlled Trial; SCFA, Short-Chain Fatty Acid; TCM, Traditional Chinese Medicine.

6 Challenges and translational prospects

Microbiota-bone axis research is still hampered by three major gaps: germ-free models fail to replicate the complexity of the human microbiota, individual metabolite receptor circadian peak phases differ by 4–6 hours, and FMT colonization is highly heterogeneous. Existing clinical evidence supports the immediate implementation of “chronotherapy” for skeletal health: taking bisphosphonates on an empty stomach in the morning increases bioavailability by 20–30%, calcium supplementation in the evening can additionally reduce nocturnal CTX by 15%, taking vitamin D with a fat-containing meal at noon is in phase with the solar rhythm, and orally administering SCFA-producing Lactobacillus reuteri in the morning increases lumbar bone density by 40% in postmenopausal women. Shift work and jet lag increase the risk of hip fractures by 32% through three pathways: reduced microbial rhythm amplitude with a phase delay of 4–6 hours, increased intestinal LPS translocation, and sustained elevation of IL-6 and TNF-α. Corresponding interventions include avoiding high-fat diets during night shifts and supplementing with resistant starch during the “biological morning” to partially restore SCFA rhythms and inhibit bone resorption. The next step is to develop CRISPR-engineered strains that continuously secrete butyrate and FXR agonists, and combine them with an AI-chronotherapy platform to analyze individual 24-hour single-cell transcriptome and plasma metabolome curves, generating a triphasic chronotherapy schedule for “drugs-nutrition-microbiota,” which will be included in Phase II randomized controlled trials to further enhance bone density benefits by one effect size.

7 Conclusion

This review elucidates how gut microbiota-derived metabolites (e.g., SCFAs, bile acids, and tryptophan derivatives) regulate bone homeostasis through a novel “metabolite–immune–bone triad” model, incorporating circadian biology to reveal rhythmic expression of receptors (e.g., GPR43, FXR) in bone stromal cells and their synchronization of osteoblastic/osteoclastic activities via epigenetic mechanisms such as H3K27ac acetylation. These insights deepen our understanding of the pathogenesis of OP and OA and provide a mechanistic foundation for targeting the GBA through precision interventions including chrononutrition, probiotics, and microbiota transplantation. Our work underscores the transformative potential of multi-omics-guided approaches and individualized temporal therapeutics for future research and clinical translation in skeletal disorders.

Edited by: Taylor Sitarik Cohen, AstraZeneca, United States

Reviewed by: Kanami Orihara, Tokyo Institute of Technology, Japan

Harold Van Bosse, Saint Louis University, United States

Author contributions

ML: Writing – review & editing, Writing – original draft. JG: Writing – original draft, Writing – review & editing. YL: Writing – original draft, Writing – review & editing. JY: Writing – original draft, Writing – review & editing. ZH: Writing – original draft, Writing – review & editing. ZL: Writing – review & editing, Writing – original draft.

Conflict of interest

The authors declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fimmu.2025.1719445/full#supplementary-material

References

  1. 1 Global, regional, and national burden of osteoarthritis, 1990–2020 and projections to 2050: a systematic analysis for the global burden of disease study 2021. Lancet Rheumatol. (2023) 5:e508–22. doi: 10.1016/S2665-9913(23)00163-7, PMID: 37675071 PMC10477960
  2. 2 MaW ChenH YuanQ ChenX LiH . Global, regional, and national epidemiology of osteoarthritis in working-age individuals: insights from the global burden of disease study 1990-2021. Sci Rep. (2025) 15:7907. doi: 10.1038/s41598-025-91783-6, PMID: 40050342 PMC11885640
  3. 3 ChenY YangC DengZ XiangT NiQ XuJ et al. . Gut microbially produced tryptophan metabolite melatonin ameliorates osteoporosis via modulating scfa and tmao metabolism. J Pineal Res. (2024) 76:e12954–79. doi: 10.1111/jpi.12954, PMID: 38618998
  4. 4 NshanianM GruberJJ GellerBS ChleilatF LancasterSM WhiteSM et al. . Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression. Nat Metab. (2025) 7:196–211. doi: 10.1038/s42255-024-01191-9, PMID: 39789354 PMC11774759
  5. 5 TicinesiA SiniscalchiC MeschiT NouvenneA . Gut microbiome and bone health: update on mechanisms, clinical correlations, and possible treatment strategies. Osteoporos Int. (2025) 36:167–91. doi: 10.1007/s00198-024-07320-0, PMID: 39643654
  6. 6 MaS WangN ZhangP WuW FuL . Fecal microbiota transplantation mitigates bone loss by improving gut microbiome composition and gut barrier function in aged rats. Peerj. (2021) 9:e12293. doi: 10.7717/peerj.12293, PMID: 34721980 PMC8542369
  7. 7 LuL TangM LiJ XieY LiY XieJ et al. . Gut microbiota and serum metabolic signatures of high-fat-induced bone loss in mice. Front Cell Infect Microbiol. (2021) 11:788576. doi: 10.3389/fcimb.2021.788576, PMID: 35004355 PMC8727351
  8. 8 GuoX ZhongK ZhangJ HuiL ZouL XueH et al. . Gut microbiota can affect bone quality by regulating serum estrogen levels. Am J Transl Res. (2022) 14:6043–55. PMC955646236247294
  9. 9 WangN MaS FuL . Gut microbiota dysbiosis as one cause of osteoporosis by impairing intestinal barrier function. Calcif Tissue Int. (2022) 110:225–35. doi: 10.1007/s00223-021-00911-7, PMID: 34480200
  10. 10 LuoB ZhouX TangQ YinY FengG LiS et al. . Circadian rhythms affect bone reconstruction by regulating bone energy metabolism. J Transl Med. (2021) 19:410. doi: 10.1186/s12967-021-03068-x, PMID: 34579752 PMC8477514
  11. 11 FujimoriK IguchiY YamashitaY GohdaK TenoN . Fxr activation accelerates early phase of osteoblast differentiation through cox-2-pge(2)-ep4 axis in bmp-2-induced mouse mesenchymal stem cells. Molecules. (2024) 30:58–76. doi: 10.3390/molecules30010058, PMID: 39795115 PMC11722014
  12. 12 GreenbaumJ LinX SuK GongR ShenH ShenJ et al. . Integration of the human gut microbiome and serum metabolome reveals novel biological factors involved in the regulation of bone mineral density. Front Cell Infect Microbiol. (2022) 12:853499. doi: 10.3389/fcimb.2022.853499, PMID: 35372129 PMC8966780
  13. 13 YanJ TakakuraA Zandi-NejadK CharlesJF . Mechanisms of gut microbiota-mediated bone remodeling. Gut Microbes. (2018) 9:84–92. doi: 10.1080/19490976.2017.1371893, PMID: 28961041 PMC5914914
  14. 14 LucasS OmataY HofmannJ BottcherM IljazovicA SarterK et al. . Short-chain fatty acids regulate systemic bone mass and protect from pathological bone loss. Nat Commun. (2018) 9:55. doi: 10.1038/s41467-017-02490-4, PMID: 29302038 PMC5754356
  15. 15 YangKL MullinsBJ LejeuneA IvanovaE ShinJ BajwaS et al. . Mitigation of osteoclast-mediated arthritic bone remodeling by short chain fatty acids. Arthritis Rheumatol. (2024) 76:647–59. doi: 10.1002/art.42765, PMID: 37994265 PMC10965381
  16. 16 YangL FanokMH Mediero-MunozA FogliLK CorciuloC AbdollahiS et al. . Augmented th17 differentiation leads to cutaneous and synovio-entheseal inflammation in a novel model of psoriatic arthritis. Arthritis Rheumatol. (2018) 70:855–67. doi: 10.1002/art.40447, PMID: 29439292 PMC5984671
  17. 17 FengB LuJ HanY HanY QiuX ZengZ . The role of short-chain fatty acids in the regulation of osteoporosis: new perspectives from gut microbiota to bone health: a review. Med (Baltimore). (2024) 103:e39471. doi: 10.1097/MD.0000000000039471, PMID: 39183408 PMC11346881
  18. 18 HanD WangW GongJ MaY LiY . Microbiota metabolites in bone: shaping health and confronting disease. Heliyon. (2024) 10:e28435. doi: 10.1016/j.heliyon.2024.e28435, PMID: 38560225 PMC10979239
  19. 19 WallimannA MagrathW ThompsonK MoriartyT RichardsRG AkdisCA et al. . Gut microbial-derived short-chain fatty acids and bone: a potential role in fracture healing. Eur Cell Mater. (2021) 41:454–70. doi: 10.22203/eCM.v041a29, PMID: 33881768 PMC9100835
  20. 20 DingK HuaF DingW . Gut microbiome and osteoporosis. Aging Dis. (2020) 11:438–47. doi: 10.14336/AD.2019.0523, PMID: 32257552 PMC7069453
  21. 21 JiJ CaiF YuanC HuangC ZhangH XuC et al. . Gut microbiota in primary osteoporosis: a systematic review. Phenomics. (2024) 4:293–7. doi: 10.1007/s43657-024-00164-y, PMID: 39398427 PMC11467150
  22. 22 CaoY GaoY HuangJ . Perturbations in gut microbiota composition in osteoporosis: a systematic review and meta-analysis. J Bone Miner Metab. (2024) 42:551–63. doi: 10.1007/s00774-024-01517-3, PMID: 38864923
  23. 23 LinX XiaoHM LiuHM LvWQ GreenbaumJ GongR et al. . Gut microbiota impacts bone via bacteroides vulgatus-valeric acid-related pathways. Nat Commun. (2023) 14:6853. doi: 10.1038/s41467-023-42005-y, PMID: 37891329 PMC10611739
  24. 24 YuilleS ReichardtN PandaS DunbarH MulderIE . Human gut bacteria as potent class i histone deacetylase inhibitors in vitro through production of butyric acid and valeric acid. PloS One. (2018) 13:e201073. doi: 10.1371/journal.pone.0201073, PMID: 30052654 PMC6063406
  25. 25 LongoUG LalliA BandiniB de SireR AngelettiS LustigS et al. . Role of the gut microbiota in osteoarthritis, rheumatoid arthritis, and spondylarthritis: an update on the gut-joint axis. Int J Mol Sci. (2024) 25:3242–58. doi: 10.3390/ijms25063242, PMID: 38542216 PMC10970477
  26. 26 YangP FengW LiC KouY LiD LiuS et al. . Lps induces fibroblast-like synoviocytes rsc-364 cells to pyroptosis through nf-kappab mediated dual signalling pathway. J Mol Histol. (2021) 52:661–9. doi: 10.1007/s10735-021-09988-8, PMID: 34085178
  27. 27 RahmanSO BariguianF MobasheriA . The potential role of probiotics in the management of osteoarthritis pain: current status and future prospects. Curr Rheumatol Rep. (2023) 25:307–26. doi: 10.1007/s11926-023-01108-7, PMID: 37656392 PMC10754743
  28. 28 JiangH LiL BaoY CaoX MaL . Microbiota in tumors: new factor influencing cancer development. Cancer Gene Ther. (2024), 1773–85. doi: 10.1038/s41417-024-00833-0, PMID: 39342031
  29. 29 JiaW LiY CheungK ZhengX . Bile acid signaling in the regulation of whole body metabolic and immunological homeostasis. Sci China Life Sci. (2024) 67:865–78. doi: 10.1007/s11427-023-2353-0, PMID: 37515688
  30. 30 ChenS XuY ZhuoW ZhangL . The emerging role of lactate in tumor microenvironment and its clinical relevance. Cancer Lett. (2024) 590:216837. doi: 10.1016/j.canlet.2024.216837, PMID: 38548215
  31. 31 BaltazarF AfonsoJ CostaM GranjaS . Lactate beyond a waste metabolite: metabolic affairs and signaling in Malignancy. Front Oncol. (2020) 10:231. doi: 10.3389/fonc.2020.00231, PMID: 32257942 PMC7093491
  32. 32 SevcikovaA MartiniakovaM OmelkaR StevurkovaV CiernikovaS . The link between the gut microbiome and bone metastasis. Int J Mol Sci. (2024) 25:12086–113. doi: 10.3390/ijms252212086, PMID: 39596154 PMC11593804
  33. 33 WuKC MccauleyKE LynchSV NayakRR KingNJ PatelS et al. . Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy. J Bone Miner Res. (2024) 39:95–105. doi: 10.1093/jbmr/zjad017, PMID: 38477719 PMC11240164
  34. 34 WangM ZhangL ChangW ZhangY . The crosstalk between the gut microbiota and tumor immunity: implications for cancer progression and treatment outcomes. Front Immunol. (2022) 13:1096551. doi: 10.3389/fimmu.2022.1096551, PMID: 36726985 PMC9885097
  35. 35 HeY HuangJ LiQ XiaW ZhangC LiuZ et al. . Gut microbiota and tumor immune escape: a new perspective for improving tumor immunotherapy. Cancers (Basel). (2022) 14:5317–37. doi: 10.3390/cancers14215317, PMID: 36358736 PMC9656981
  36. 36 KyriaziAA KaraglaniM AgelakiS BaritakiS . Intratumoral microbiome: foe or friend in reshaping the tumor microenvironment landscape? Cells. (2024) 13:1279–316. doi: 10.3390/cells13151279, PMID: 39120310 PMC11312414
  37. 37 TominariT MatsumotoC TanakaY ShimizuK TakatoyaM SugasakiM et al. . Roles of toll-like receptor signaling in inflammatory bone resorption. Biol (Basel). (2024) 13:692–707. doi: 10.3390/biology13090692, PMID: 39336119 PMC11429252
  38. 38 JinS JiangH SunY LiF XiaJ LiY et al. . Osteogenic differentiation of periodontal membrane stem cells in inflammatory environments. Open Life Sci. (2022) 17:1240–8. doi: 10.1515/biol-2022-0474, PMID: 36213382 PMC9490861
  39. 39 GoudarziF KianiA NamiY ShahmohammadiA MohammadalipourA KaramiA et al. . Potential probiotic lactobacillus delbrueckii subsp. Lactis kums-y33 suppresses adipogenesis and promotes osteogenesis in human adipose-derived mesenchymal stem cell. Sci Rep. (2024) 14:9689. doi: 10.1038/s41598-024-60061-2, PMID: 38678043 PMC11055903
  40. 40 LaiJ GongL LiuY ZhangX LiuW HanM et al. . Associations between gut microbiota and osteoporosis or osteopenia in a cohort of chinese han youth. Sci Rep. (2024) 14:20948. doi: 10.1038/s41598-024-71731-6, PMID: 39251661 PMC11385745
  41. 41 KapoorS GuptaM SapraL KaurT SrivastavaRK . Delineating the nexus between gut-intratumoral microbiome and osteo-immune system in bone metastases. Bone Rep. (2024) 23:101809. doi: 10.1016/j.bonr.2024.101809, PMID: 39497943 PMC11532283
  42. 42 RamosMG SamoudaH BohnT . Short chain fatty acid metabolism in relation to gut microbiota and genetic variability. Nutrients. (2022) 14:5361–409. doi: 10.3390/nu14245361, PMID: 36558520 PMC9788597
  43. 43 ZietekM CelewiczZ SzczukoM . Short-chain fatty acids, maternal microbiota and metabolism in pregnancy. Nutrients. (2021) 13:1244–64. doi: 10.3390/nu13041244, PMID: 33918804 PMC8069164
  44. 44 IkedaT NishidaA YamanoM KimuraI . Short-chain fatty acid receptors and gut microbiota as therapeutic targets in metabolic, immune, and neurological diseases. Pharmacol Ther. (2022) 239:108273. doi: 10.1016/j.pharmthera.2022.108273, PMID: 36057320
  45. 45 LiF TaiL SunX LvZ TangW WangT et al. . Molecular recognition and activation mechanism of short-chain fatty acid receptors ffar2/3. Cell Res. (2024) 34:323–6. doi: 10.1038/s41422-023-00914-z, PMID: 38191689 PMC10978569
  46. 46 SchroederTM WestendorfJJ . Histone deacetylase inhibitors promote osteoblast maturation. J Bone Miner Res. (2005) 20:2254–63. doi: 10.1359/JBMR.050813, PMID: 16294278
  47. 47 ParkJ KimM KangSG JannaschAH CooperB PattersonJ et al. . Short-chain fatty acids induce both effector and regulatory t cells by suppression of histone deacetylases and regulation of the mtor-s6k pathway. Mucosal Immunol. (2015) 8:80–93. doi: 10.1038/mi.2014.44, PMID: 24917457 PMC4263689
  48. 48 DongQ FuH LiW JiX YinY ZhangY et al. . Nuclear farnesoid x receptor protects against bone loss by driving osteoblast differentiation through stabilizing runx2. Bone Res. (2025) 13:20. doi: 10.1038/s41413-024-00394-w, PMID: 39885145 PMC11782663
  49. 49 TuY YangR XuX ZhouX . The microbiota-gut-bone axis and bone health. J Leukoc Biol. (2021) 110:525–37. doi: 10.1002/JLB.3MR0321-755R, PMID: 33884666
  50. 50 FanM XuY WuB LongJ LiuC LiangZ et al. . Geniposidic acid targeting fxr “s332 and h447” mediated conformational change to upregulate cyps and mir-19a-3p to ameliorate drug-induced liver injury. Adv Sci (Weinh). (2025), e2409107-26. doi: 10.1002/advs.202409107, PMID: 39998442 PMC12005789
  51. 51 LiuM JinF ZhangS LiS ZhuD CuiY et al. . Activation of farnesoid x receptor signaling by geniposidic acid promotes osteogenesis. Phytomedicine. (2022) 103:154258. doi: 10.1016/j.phymed.2022.154258, PMID: 35716540
  52. 52 ZhangY CaoM LiY LuP DaiG ZhangM et al. . Fecal microbiota transplantation ameliorates bone loss in mice with ovariectomy-induced osteoporosis via modulating gut microbiota and metabolic function. J Orthop Translat. (2022) 37:46–60. doi: 10.1016/j.jot.2022.08.003, PMID: 36196151 PMC9520092
  53. 53 LiJ YangM LuC HanJ TangS ZhouJ et al. . Tuna bone powder alleviates glucocorticoid-induced osteoporosis via coregulation of the nf-kappab and wnt/beta-catenin signaling pathways and modulation of gut microbiota composition and metabolism. Mol Nutr Food Res. (2020) 64:e1900861. doi: 10.1002/mnfr.201900861, PMID: 31953894
  54. 54 WangX QuZ ZhaoS LuoL YanL . Wnt/beta-catenin signaling pathway: proteins’ roles in osteoporosis and cancer diseases and the regulatory effects of natural compounds on osteoporosis. Mol Med. (2024) 30:193. doi: 10.1186/s10020-024-00957-x, PMID: 39468464 PMC11520425
  55. 55 ZengD UmarM ZhuZ PanH LuWW XiaoG et al. . Development of novel osteoarthritis therapy by targeting ampk-beta-catenin-runx2 signaling. Genes Dis. (2025) 12:101247. doi: 10.1016/j.gendis.2024.101247, PMID: 39552787 PMC11566674
  56. 56 AryaPN SaranyaI SelvamuruganN . Runx2 regulation in osteoblast differentiation: a possible therapeutic function of the lncrna and mirna-mediated network. Differentiation. (2024) 140:100803. doi: 10.1016/j.diff.2024.100803, PMID: 39089986
  57. 57 HuL ChenW QianA LiYP . Wnt/beta-catenin signaling components and mechanisms in bone formation. Homeost Dis Bone Res. (2024) 12:39. doi: 10.1038/s41413-024-00342-8, PMID: 38987555 PMC11237130
  58. 58 KobayashiY IwamotoR HeZ UdagawaN . Wnt family members regulating osteogenesis and their origins. J Bone Miner Metab. (2025) 43:39–45. doi: 10.1007/s00774-024-01554-y, PMID: 39283365 PMC11954845
  59. 59 SongJ ChangW WangY GaoP ZhangJ XiaoZ et al. . Inhibitors of the wnt pathway in osteoporosis: a review of mechanisms of action and potential as therapeutic targets. Biomol BioMed. (2025) 25:511–24. doi: 10.17305/bb.2024.11200, PMID: 39606935 PMC12010972
  60. 60 SrivastavaRK SapraL MishraPK . Osteometabolism: metabolic alterations in bone pathologies. Cells (Basel Switzerland). (2022) 11:3943. doi: 10.3390/cells11233943, PMID: 36497201 PMC9735555
  61. 61 ZhangP LiX LiangJ ZhengY TongY ShenJ et al. . Chenodeoxycholic acid modulates cholestatic niche through fxr/myc/p-selectin axis in liver endothelial cells. Nat Commun. (2025) 16:2093. doi: 10.1038/s41467-025-57351-2, PMID: 40025016 PMC11873286
  62. 62 AlunnoA ManettiM CaterbiS Ibba-ManneschiL BistoniO BartoloniE et al. . Altered immunoregulation in rheumatoid arthritis: the role of regulatory t cells and proinflammatory th17 cells and therapeutic implications. Mediators Inflammation. (2015) 2015:751793. doi: 10.1155/2015/751793, PMID: 25918479 PMC4397010
  63. 63 LochmannD RichardsonT . Selective serotonin reuptake inhibitors. Handb Exp Pharmacol. (2019) 250:135–44. doi: 10.1007/164_2018_172, PMID: 30838457
  64. 64 ChenC CaoZ LeiH ZhangC WuM HuangS et al. . Microbial tryptophan metabolites ameliorate ovariectomy-induced bone loss by repairing intestinal ahr-mediated gut-bone signaling pathway. Adv Sci (Weinh). (2024) 11:e2404545. doi: 10.1002/advs.202404545, PMID: 39041942 PMC11423200
  65. 65 JingW DongS XuY LiuJ RenJ LiuX et al. . Gut microbiota-derived tryptophan metabolites regulated by wuji wan to attenuate colitis through ahr signaling activation. Acta Pharm Sin B. (2025) 15:205–23. doi: 10.1016/j.apsb.2024.11.009, PMID: 40041900 PMC11873645
  66. 66 HouY LiJ YingS . Tryptophan metabolism and gut microbiota: a novel regulatory axis integrating the microbiome, immunity, and cancer. Metabolites. (2023) 13:1166–84. doi: 10.3390/metabo13111166, PMID: 37999261 PMC10673612
  67. 67 KonopelskiP MogilnickaI . Biological effects of indole-3-propionic acid, a gut microbiota-derived metabolite, and its precursor tryptophan in mammals’ health and disease. Int J Mol Sci. (2022) 23:1222–41. doi: 10.3390/ijms23031222, PMID: 35163143 PMC8835432
  68. 68 KimJ CheX KimS ChoiJ LeeJH LeeJ et al. . Sericin’s potential in osteoporosis management: the roles of l-serine and d-serine in bone metabolism regulation. Nutrients. (2025) 17:574–91. doi: 10.3390/nu17030574, PMID: 39940432 PMC11820189
  69. 69 AnayaJM BollagWB HamrickMW IsalesCM . The role of tryptophan metabolites in musculoskeletal stem cell aging. Int J Mol Sci. (2020) 21:6670–84. doi: 10.3390/ijms21186670, PMID: 32933099 PMC7555967
  70. 70 LiuZ XuX ShenY HaoY CuiW LiW et al. . Altered gut microbiota and metabolites profile are associated with reduced bone metabolism in ethanol-induced osteoporosis. Cell Prolif. (2022) 55:e13245. doi: 10.1111/cpr.13245, PMID: 35688648 PMC9251047
  71. 71 Gomez-De-Tejada-RomeroM Murias-HenriquezC Saavedra-SantanaP Sablon-GonzalezN AbreuDR Sosa-HenriquezM . Influence of serum uric acid on bone and fracture risk in postmenopausal women. Aging Clin Exp Res. (2024) 36:156. doi: 10.1007/s40520-024-02819-2, PMID: 39085733 PMC11291523
  72. 72 SongS CaiX HuJ ZhuQ ShenD MaH et al. . Serum uric acid and bone health in middle-aged and elderly hypertensive patients: a potential u-shaped association and implications for future fracture risk. Metabolites. (2025) 15:15–32. doi: 10.3390/metabo15010015, PMID: 39852358 PMC11766991
  73. 73 ZaichkoNV MelnikAV YoltukhivskyyMM OlhovskiyAS PalamarchukIV . Hydrogen sulfide: metabolism, biological and medical role. Ukr Biochem J. (2014) 86:5–25. doi: 10.15407/ubj86.05.005 25816584
  74. 74 ZhaoY CaoG GuoL ChengQ . Hydrogen sulfide ameliorates myocardial injury caused by sepsis through suppressing ros-mediated endoplasmic reticulum stress. Sichuan Da Xue Xue Bao Yi Xue Ban. (2022) 53:798–804. doi: 10.12182/20220960106, PMID: 36224681 PMC10408801
  75. 75 PowellCR DillonKM MatsonJB . A review of hydrogen sulfide (h(2)s) donors: chemistry and potential therapeutic applications. Biochem Pharmacol. (2018) 149:110–23. doi: 10.1016/j.bcp.2017.11.014, PMID: 29175421 PMC5866188
  76. 76 ZhuZ LianX BhatiaM . Hydrogen sulfide: a gaseous mediator and its key role in programmed cell death, oxidative stress, inflammation and pulmonary disease. Antioxid (Basel). (2022) 11:2162–83. doi: 10.3390/antiox11112162, PMID: 36358533 PMC9687070
  77. 77 XuX FuH QuanH LiY ChenQ QuD et al. . Effects of fructooligosaccharides and lactobacillus reuteri on the composition and metabolism of gut microbiota in students. Food Funct. (2025) 16:1562–75. doi: 10.1039/D4FO03763D, PMID: 39912125
  78. 78 SapraL DarHY BhardwajA PandeyA KumariS AzamZ et al. . Lactobacillus rhamnosus attenuates bone loss and maintains bone health by skewing treg-th17 cell balance in ovx mice. Sci Rep. (2021) 11:1807. doi: 10.1038/s41598-020-80536-2, PMID: 33469043 PMC7815799
  79. 79 GuoM LiuH YuY ZhuX XieH WeiC et al. . Lactobacillus rhamnosus gg ameliorates osteoporosis in ovariectomized rats by regulating the th17/treg balance and gut microbiota structure. Gut Microbes. (2023) 15:2190304. doi: 10.1080/19490976.2023.2190304, PMID: 36941563 PMC10038048
  80. 80 ChasovV GilyazovaE GaneevaI ZmievskayaE DavletshinD ValiullinaA et al. . Gut microbiota modulation: a novel strategy for rheumatoid arthritis therapy. Biomolecules. (2024) 14:1653–76. doi: 10.3390/biom14121653, PMID: 39766360 PMC11674688
  81. 81 LiJ FanR ZhangZ ZhaoL HanY ZhuY et al. . Role of gut microbiota in rheumatoid arthritis: potential cellular mechanisms regulated by prebiotic, probiotic, and pharmacological interventions. Microbiol Res. (2025) 290:127973. doi: 10.1016/j.micres.2024.127973, PMID: 39541714
  82. 82 QiP XieR LiuH ZhangZ ChengY MaJ et al. . Mechanisms of gut homeostasis regulating th17/treg cell balance in pmop. Front Immunol. (2024) 15:1497311. doi: 10.3389/fimmu.2024.1497311, PMID: 39735544 PMC11671525
  83. 83 BrittonRA IrwinR QuachD SchaeferL ZhangJ LeeT et al. . Probiotic l. Reuteri treatment prevents bone loss in a menopausal ovariectomized mouse model. J Cell Physiol. (2014) 229:1822–30. doi: 10.1002/jcp.24636, PMID: 24677054 PMC4129456
  84. 84 NilssonAG SundhD BackhedF LorentzonM . Lactobacillus reuteri reduces bone loss in older women with low bone mineral density: a randomized, placebo-controlled, double-blind, clinical trial. J Intern Med. (2018) 284:307–17. doi: 10.1111/joim.12805, PMID: 29926979
  85. 85 YangW WangY MoK ChenW XieX . Single-cell rna sequencing reveals multiple immune cell subpopulations promote the formation of abnormal bone microenvironment in osteoporosis. Sci Rep. (2024) 14:29493. doi: 10.1038/s41598-024-80993-z, PMID: 39604551 PMC11603148
  86. 86 AmarasekaraDS YuJ RhoJ . Bone loss triggered by the cytokine network in inflammatory autoimmune diseases. J Immunol Res. (2015) 2015:832127. doi: 10.1155/2015/832127, PMID: 26065006 PMC4434203
  87. 87 ZhouP ZhengT ZhaoB . Cytokine-mediated immunomodulation of osteoclastogenesis. Bone. (2022) 164:116540. doi: 10.1016/j.bone.2022.116540, PMID: 36031187 PMC10657632
  88. 88 Le GoffB BouvardB LequerreT LespessaillesE MarotteH PersY et al. . Implication of il-17 in bone loss and structural damage in inflammatory rheumatic diseases. Mediators Inflammation. (2019) 2019:8659302. doi: 10.1155/2019/8659302, PMID: 31485194 PMC6710740
  89. 89 YuW SunS FuQ . The role of short-chain fatty acid in metabolic syndrome and its complications: focusing on immunity and inflammation. Front Immunol. (2025) 16:1519925. doi: 10.3389/fimmu.2025.1519925, PMID: 39991152 PMC11842938
  90. 90 ChenJ JiaS XueX GuoC DongK . Gut microbiota: a novel target for exercise-mediated regulation of nlrp3 inflammasome activation. Front Microbiol. (2024) 15:1476908. doi: 10.3389/fmicb.2024.1476908, PMID: 39834360 PMC11743191
  91. 91 KarimiM ShirsalimiN HashempourZ Salehi OmranH SedighiE BeigiF et al. . Safety and efficacy of fecal microbiota transplantation (fmt) as a modern adjuvant therapy in various diseases and disorders: a comprehensive literature review. Front Immunol. (2024) 15:1439176. doi: 10.3389/fimmu.2024.1439176, PMID: 39391303 PMC11464302
  92. 92 FehilySR BasnayakeC WrightEK KammMA . Fecal microbiota transplantation therapy in crohn’s disease: systematic review. J Gastroenterol Hepatol. (2021) 36:2672–86. doi: 10.1111/jgh.15598, PMID: 34169565
  93. 93 GuoM TanL NieX ZhuX PanY GaoZ . The pmt2p-mediated protein o-mannosylation is required for morphogenesis, adhesive properties, cell wall integrity and full virulence of magnaporthe oryzae. Front Microbiol. (2016) 7:630. doi: 10.3389/fmicb.2016.00630, PMID: 27199956 PMC4852298
  94. 94 WollmuthEM AngertER . Microbial circadian clocks: host-microbe interplay in diel cycles. BMC Microbiol. (2023) 23:124. doi: 10.1186/s12866-023-02839-4, PMID: 37161348 PMC10173096
  95. 95 BrooksJFN BehrendtCL RuhnKA LeeS RajP TakahashiJS et al. . The microbiota coordinates diurnal rhythms in innate immunity with the circadian clock. Cell. (2021) 184:4154–67. doi: 10.1016/j.cell.2021.07.001, PMID: 34324837 PMC8967342
  96. 96 LeeD KimM HanJ . Gpr41 and gpr43: from development to metabolic regulation. BioMed Pharmacother. (2024) 175:116735. doi: 10.1016/j.biopha.2024.116735, PMID: 38744220
  97. 97 CaiX RenF YaoY . Gut microbiota and their metabolites in the immune response of rheumatoid arthritis: therapeutic potential and future directions. Int Immunopharmacol. (2025) 147:114034. doi: 10.1016/j.intimp.2025.114034, PMID: 39805176
  98. 98 ZhaoY ChenF WuW SunM BilottaAJ YaoS et al. . Gpr43 mediates microbiota metabolite scfa regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mtor and stat3. Mucosal Immunol. (2018) 11:752–62. doi: 10.1038/mi.2017.118, PMID: 29411774 PMC5976519
  99. 99 BeheraJ IsonJ TyagiSC TyagiN . The role of gut microbiota in bone homeostasis. Bone. (2020) 135:115317. doi: 10.1016/j.bone.2020.115317, PMID: 32169602 PMC8457311
  100. 100 MannER LamYK UhligHH . Short-chain fatty acids: linking diet. Microb Immun Nat Rev Immunol. (2024) 24:577–95. doi: 10.1038/s41577-024-01014-8, PMID: 38565643
  101. 101 VoigtRM ForsythCB KeshavarzianA . Circadian rhythms: a regulator of gastrointestinal health and dysfunction. Expert Rev Gastroenterol Hepatol. (2019) 13:411–24. doi: 10.1080/17474124.2019.1595588, PMID: 30874451 PMC6533073
  102. 102 ZengY GuoZ WuM ChenF ChenL . Circadian rhythm regulates the function of immune cells and participates in the development of tumors. Cell Death Discov. (2024) 10:199. doi: 10.1038/s41420-024-01960-1, PMID: 38678017 PMC11055927
  103. 103 BarriosBE JaimeCE SenaAA de Paula-SilvaM GilCD OlianiSM et al. . Brief disruption of circadian rhythms alters intestinal barrier integrity and modulates dss-induced colitis severity in mice. Inflammation. (2024), 1900–11. doi: 10.1007/s10753-024-02162-8, PMID: 39407037
  104. 104 HuT LiuC LeiM ZengQ LiL TangH et al. . Metabolic regulation of the immune system in health and diseases: mechanisms and interventions. Signal Transduct Target Ther. (2024) 9:268. doi: 10.1038/s41392-024-01954-6, PMID: 39379377 PMC11461632
  105. 105 XuZ WangX XiaoD HuL LuM WuZ et al. . Hydrogen sulfide protects mc3t3-e1 osteoblastic cells against h2o2-induced oxidative damage-implications for the treatment of osteoporosis. Free Radic Biol Med. (2011) 50:1314–23. doi: 10.1016/j.freeradbiomed.2011.02.016, PMID: 21354302
  106. 106 WadhwaR KumarM TalegaonkarS VohoraD . Serotonin reuptake inhibitors and bone health: a review of clinical studies and plausible mechanisms. Osteoporos Sarcopenia. (2017) 3:75–81. doi: 10.1016/j.afos.2017.05.002, PMID: 30775508 PMC6372777
  107. 107 YadavVK BalajiS SureshPS LiuXS LuX LiZ et al. . Pharmacological inhibition of gut-derived serotonin synthesis is a potential bone anabolic treatment for osteoporosis. Nat Med. (2010) 16:308–12. doi: 10.1038/nm.2098, PMID: 20139991 PMC2836724
  108. 108 SunQ XuL HuZ LiuJ YuT LiM et al. . Melatonin regulates osteoblast differentiation through the m6a reader hnrnpa2b1 under simulated microgravity. Curr Issues Mol Biol. (2024) 46:9624–38. doi: 10.3390/cimb46090572, PMID: 39329924 PMC11430354
  109. 109 YangW JinM GuY ZhaoX ZhuL HeS et al. . Intracellular osteopontin potentiates the immunosuppressive activity of mesenchymal stromal cells. Stem Cell Res Ther. (2024) 15:366. doi: 10.1186/s13287-024-03979-8, PMID: 39407354 PMC11475537
  110. 110 BraunT ZwerinaJ . Positive regulators of osteoclastogenesis and bone resorption in rheumatoid arthritis. Arthritis Res Ther. (2011) 13:235. doi: 10.1186/ar3380, PMID: 21861862 PMC3239343
  111. 111 GreenblattMB TsaiJN WeinMN . Bone turnover markers in the diagnosis and monitoring of metabolic bone disease. Clin Chem. (2017) 63:464–74. doi: 10.1373/clinchem.2016.259085, PMID: 27940448 PMC5549920
  112. 112 CastanedaM StrongJM AlabiDA HernandezCJ . The gut microbiome and bone strength. Curr Osteoporos Rep. (2020) 18:677–83. doi: 10.1007/s11914-020-00627-x, PMID: 33030683 PMC7736097
  113. 113 HansdahK LuiJC . Emerging insights into the endocrine regulation of bone homeostasis by gut microbiome. J Endocr Soc. (2024) 8:bvae117. doi: 10.1210/jendso/bvae117, PMID: 38957653 PMC11215793
  114. 114 AziziehFY ShehabD JarallahKA GuptaR RaghupathyR . Circulatory levels of rankl, opg, and oxidative stress markers in postmenopausal women with normal or low bone mineral density. biomark Insights. (2019) 14:90826255. doi: 10.1177/1177271919843825, PMID: 31452599 PMC6700864
  115. 115 ThaissCA ZeeviD LevyM Zilberman-SchapiraG SuezJ TengelerAC et al. . Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell. (2014) 159:514–29. doi: 10.1016/j.cell.2014.09.048, PMID: 25417104
  116. 116 ThaissCA LevyM KoremT DohnalovaL ShapiroH JaitinDA et al. . Microbiota diurnal rhythmicity programs host transcriptome oscillations. Cell. (2016) 167:1495–510. doi: 10.1016/j.cell.2016.11.003, PMID: 27912059
  117. 117 FeskanichD HankinsonSE SchernhammerES . Nightshift work and fracture risk: the nurses’ health study. Osteoporos Int. (2009) 20:537–42. doi: 10.1007/s00198-008-0729-5, PMID: 18766292 PMC2651998
  118. 118 ArcherSN RobilliardDL SkeneDJ SmitsM WilliamsA ArendtJ et al. . A length polymorphism in the circadian clock gene per3 is linked to delayed sleep phase syndrome and extreme diurnal preference. Sleep. (2003) 26:413–5. doi: 10.1093/sleep/26.4.413, PMID: 12841365
  119. 119 YamazakiS StraumeM TeiH SakakiY MenakerM BlockGD . Effects of aging on central and peripheral mammalian clocks. Proc Natl Acad Sci U.S.A. (2002) 99:10801–6. doi: 10.1073/pnas.152318499, PMID: 12149444 PMC125050
  120. 120 WangH TianG PeiZ YuX WangY XuF et al. . Bifidobacterium longum increases serum vitamin d metabolite levels and modulates intestinal flora to alleviate osteoporosis in mice. Msphere. (2025) 10:e103924. doi: 10.1128/msphere.01039-24, PMID: 39982061 PMC11934329
  121. 121 Sanchez-LanzasR Jimenez-PompaA GanuzaM . The evolving hematopoietic niche during development. Front Mol Biosci. (2024) 11:1488199. doi: 10.3389/fmolb.2024.1488199, PMID: 39417006 PMC11480086
  122. 122 BihletAR ByrjalsenI Bay-JensenA AndersenJR ChristiansenC RiisBJ et al. . Associations between biomarkers of bone and cartilage turnover, gender, pain categories and radiographic severity in knee osteoarthritis. Arthritis Res Ther. (2019) 21:203. doi: 10.1186/s13075-019-1987-7, PMID: 31481084 PMC6724319
  123. 123 IshijimaM KanekoH KanekoK . The evolving role of biomarkers for osteoarthritis. Ther Adv Musculoskelet Dis. (2014) 6:144–53. doi: 10.1177/1759720X14541175, PMID: 25342994 PMC4206655
  124. 124 ChoiY LeeD LimH JeongJ SonnJ KangS et al. . Interleukin-1beta stimulates matrix metalloproteinase-2 expression via a prostaglandin e2-dependent mechanism in human chondrocytes. Exp Mol Med. (2004) 36:226–32. doi: 10.1038/emm.2004.31, PMID: 15272234
  125. 125 SunC ZhouX GuoT MengJ . The immune role of the intestinal microbiome in knee osteoarthritis: a review of the possible mechanisms and therapies. Front Immunol. (2023) 14:1168818. doi: 10.3389/fimmu.2023.1168818, PMID: 37388748 PMC10306395
  126. 126 LiuS XuH LiuL MaW FanH LiuF et al. . Gut microbiome dysbiosis accelerates osteoarthritis progression by inducing ifp-sm inflammation in “double-hit” mice. Arthritis Res Ther. (2025) 27:137. doi: 10.1186/s13075-025-03602-y, PMID: 40624668 PMC12232632
  127. 127 LvX DengX LaiR LiuS ZouZ DaiX et al. . The association between dietary fiber intake and osteoarthritis: a cross-sectional study from the 1999–2018 u.s. National health and nutrition examination survey. J Orthop Surg Res. (2025) 20:209. doi: 10.1186/s13018-025-05625-2, PMID: 40016809 PMC11869705
  128. 128 YiC HuangS ZhangW GuoL XiaT HuangF et al. . Synergistic interactions between gut microbiota and short chain fatty acids: pioneering therapeutic frontiers in chronic disease management. Microb Pathog. (2025) 199:107231. doi: 10.1016/j.micpath.2024.107231, PMID: 39681288
  129. 129 IbrahimI SyamalaS AyarigaJA XuJ RobertsonBK MeenakshisundaramS et al. . Modulatory effect of gut microbiota on the gut-brain, gut-bone axes, and the impact of cannabinoids. Metabolites. (2022) 12:1247–77. doi: 10.3390/metabo12121247, PMID: 36557285 PMC9781427
  130. 130 JakemanSA HenryCN MartinBR MccabeGP MccabeLD JacksonGS et al. . Soluble corn fiber increases bone calcium retention in postmenopausal women in a dose-dependent manner: a randomized crossover trial. Am J Clin Nutr. (2016) 104:837–43. doi: 10.3945/ajcn.116.132761, PMID: 27465372
  131. 131 Fernández-MurgaML OlivaresM SanzY . Bifidobacterium pseudocatenulatum cect 7765 reverses the adverse effects of diet-induced obesity through the gut-bone axis. Bone. (2020) 141:115580. doi: 10.1016/j.bone.2020.115580, PMID: 32795675
  132. 132 MinkoffNZ AslamS MedinaM Tanner-SmithEE ZackularJP AcraS et al. . Fecal microbiota transplantation for the treatment of recurrent clostridioides difficile (clostridium difficile). Cochrane Database Syst Rev. (2023) 4:CD13871. doi: 10.1002/14651858.CD013871.pub2, PMID: 37096495 PMC10125800
  133. 133 WuT ShuT KangL WuJ XingJ LuZ et al. . Icaritin, a novel plant-derived osteoinductive agent, enhances the osteogenic differentiation of human bone marrow- and human adipose tissue-derived mesenchymal stem cells. Int J Mol Med. (2017) 39:984–92. doi: 10.3892/ijmm.2017.2906, PMID: 28260001
  134. 134 LuoJ ZhuJ WangL KangJ WangX XiongJ . Co-electrospun nano-/microfibrous composite scaffolds with structural and chemical gradients for bone tissue engineering. Mater Sci Eng C Mater Biol Appl. (2021) 119:111622. doi: 10.1016/j.msec.2020.111622, PMID: 33321664
  135. 135 GeYW LuJW SunZY LiuZQ ZhouJ KeQF et al. . Ursolic acid loaded-mesoporous bioglass/chitosan porous scaffolds as drug delivery system for bone regeneration. Nanomed (Lond). (2019) 18:336–46. doi: 10.1016/j.nano.2018.10.010, PMID: 30419364
  136. 136 WuY CaoL XiaL WuQ WangJ WangX et al. . Evaluation of osteogenesis and angiogenesis of icariin in local controlled release and systemic delivery for calvarial defect in ovariectomized rats. Sci Rep. (2017) 7:5077. doi: 10.1038/s41598-017-05392-z, PMID: 28698566 PMC5505963
  137. 137 ZhangY CaoM LiY ZhangR WuM YuQ et al. . Fecal microbiota transplantation as a promising treatment option for osteoporosis. J Bone Miner Metab. (2022) 40:874–89. doi: 10.1007/s00774-022-01375-x, PMID: 36357745 PMC9649400
  138. 138 MaP WangR ChenH ZhengJ YangW MengB et al. . Fecal microbiota transplantation alleviates lipopolysaccharide-induced osteoporosis by modulating gut microbiota and long non-coding rna tug1 expression. Front Cell Infect Microbiol. (2025) 15:1535666. doi: 10.3389/fcimb.2025.1535666, PMID: 40292220 PMC12021831
  139. 139 ArpornmaeklongP SareethammanuwatM ApinyauppathamK BoonyuenS . Characteristics and biologic effects of thermosensitive quercetin-chitosan/collagen hydrogel on human periodontal ligament stem cells. J BioMed Mater Res B Appl Biomater. (2021) 109:1656–70. doi: 10.1002/jbm.b.34823, PMID: 33644957
  140. 140 ZhouT WangM MaH LiX HeianzaY QiL . Dietary fiber, genetic variations of gut microbiota-derived short-chain fatty acids, and bone health in uk biobank. J Clin Endocrinol Metab. (2021) 106:201–10. doi: 10.1210/clinem/dgaa740, PMID: 33051670 PMC8186524
  141. 141 CyranoskiD . China to roll back regulations for traditional medicine despite safety concerns. Nature. (2017) 551:552–3. doi: 10.1038/nature.2017.23038, PMID: 29189784
  142. 142 DoppJ OrtegaA DavieK PoovathingalS BazE LiuS . Single-cell transcriptomics reveals that glial cells integrate homeostatic and circadian processes to drive sleep-wake cycles. Nat Neurosci. (2024) 27:359–72. doi: 10.1038/s41593-023-01549-4, PMID: 38263460 PMC10849968
  143. 143 ZhuM WangQ YangY LiuX ZhangJ LiG et al. . Multiomics approach reveals the comprehensive interactions between nutrition and children’s gut microbiota, and microbial and host metabolomes. Nutr J. (2025) 24:50. doi: 10.1186/s12937-025-01116-6, PMID: 40158160 PMC11954295
  144. 144 YanJ CharlesJF . Gut microbiome and bone: to build, destroy, or both? Curr Osteoporos Rep. (2017) 15:376–84. doi: 10.1007/s11914-017-0382-z, PMID: 28620867 PMC5538387
  145. 145 YanJ HerzogJW TsangK BrennanCA BowerMA GarrettWS et al. . Gut microbiota induce igf-1 and promote bone formation and growth. Proc Natl Acad Sci U.S.A. (2016) 113:E7554–63. doi: 10.1073/pnas.1607235113, PMID: 27821775 PMC5127374
  146. 146 SunM WuW LiuZ CongY . Microbiota metabolite short chain fatty acids, gpcr, and inflammatory bowel diseases. J Gastroenterol. (2017) 52:1–8. doi: 10.1007/s00535-016-1242-9, PMID: 27448578 PMC5215992
  147. 147 MeyerC BrockmuellerA RuizDPV ShakibaeiM . Microbiota and resveratrol: how are they linked to osteoporosis? Cells. (2024) 13:1145–89. doi: 10.3390/cells13131145, PMID: 38994996 PMC11240679
  148. 148 WuY ZhangX LiuX ZhaoZ TaoS XuQ et al. . Galactooligosaccharides and limosilactobacillus reuteri synergistically alleviate gut inflammation and barrier dysfunction by enriching bacteroides acidifaciens for pentadecanoic acid biosynthesis. Nat Commun. (2024) 15:9291. doi: 10.1038/s41467-024-53144-1, PMID: 39468026 PMC11519483
  149. 149 LyuZ HuY GuoY LiuD . Modulation of bone remodeling by the gut microbiota: a new therapy for osteoporosis. Bone Res. (2023) 11:31. doi: 10.1038/s41413-023-00264-x, PMID: 37296111 PMC10256815
  150. 150 KimI ParkS KimJ ParkSY SeoJ RohS . Treatment with lactobacillus paracasei l30 extract induces osteogenic differentiation of human bone marrow mesenchymal stem cells in vitro. BioMed Pharmacother. (2025) 184:117913. doi: 10.1016/j.biopha.2025.117913, PMID: 39955853
  151. 151 ZhangZ MocanuV DeehanEC HotteN ZhuY WeiS et al. . Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial. Gut Microbes. (2024) 16:2345134. doi: 10.1080/19490976.2024.2345134, PMID: 38685731 PMC11062372
  152. 152 FangH FuL WangJ . Protocol for fecal microbiota transplantation in inflammatory bowel disease: a systematic review and meta-analysis. BioMed Res Int. (2018) 2018:8941340. doi: 10.1155/2018/8941340, PMID: 30302341 PMC6158944
  153. 153 VermeireS JoossensM VerbekeK WangJ MachielsK SabinoJ et al. . Donor species richness determines faecal microbiota transplantation success in inflammatory bowel disease. J Crohns Colitis. (2016) 10:387–94. doi: 10.1093/ecco-jcc/jjv203, PMID: 26519463 PMC4946755
  154. 154 DaoMC EverardA Aron-WisnewskyJ SokolovskaN PriftiE VergerEO et al. . Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut. (2016) 65:426–36. doi: 10.1136/gutjnl-2014-308778, PMID: 26100928
  155. 155 SokolH PigneurB WatterlotL LakhdariO Bermudez-HumaranLG GratadouxJ et al. . Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of crohn disease patients. Proc Natl Acad Sci U.S.A. (2008) 105:16731–6. doi: 10.1073/pnas.0804812105, PMID: 18936492 PMC2575488
  156. 156 SteinRR BucciV ToussaintNC BuffieCG RatschG PamerEG et al. . Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PloS Comput Biol. (2013) 9:e1003388. doi: 10.1371/journal.pcbi.1003388, PMID: 24348232 PMC3861043
  157. 157 YadegarA Bar-YosephH MonaghanTM PakpourS SeverinoA KuijperEJ et al. . Fecal microbiota transplantation: current challenges and future landscapes. Clin Microbiol Rev. (2024) 37:e6022. doi: 10.1128/cmr.00060-22, PMID: 38717124 PMC11325845
  158. 158 HwangD ChongE LiY LiY RohK . Deciphering the gut microbiome’s metabolic code: pathways to bone health and novel therapeutic avenues. Front Endocrinol (Lausanne). (2025) 16:1553655. doi: 10.3389/fendo.2025.1553655, PMID: 40475999 PMC12137108
  159. 159 PengS ZhangG HeY WangX LeungP LeungK et al. . Epimedium-derived flavonoids promote osteoblastogenesis and suppress adipogenesis in bone marrow stromal cells while exerting an anabolic effect on osteoporotic bone. Bone. (2009) 45:534–44. doi: 10.1016/j.bone.2009.05.022, PMID: 19501202
  160. 160 TsengP HouS ChenR PengH HsiehC KuoM et al. . Resveratrol promotes osteogenesis of human mesenchymal stem cells by upregulating runx2 gene expression via the sirt1/foxo3a axis. J Bone Miner Res. (2011) 26:2552–63. doi: 10.1002/jbmr.460, PMID: 21713995
  161. 161 MohammadzadehM ZareiM AbbasiH WebsterTJ BeheshtizadehN . Promoting osteogenesis and bone regeneration employing icariin-loaded nanoplatforms. J Biol Eng. (2024) 18:29. doi: 10.1186/s13036-024-00425-4, PMID: 38649969 PMC11036660
  162. 162 SuY ChenK HassanshahiM TangQ HowePR XianCJ . Childhood cancer chemotherapy-induced bone damage: pathobiology and protective effects of resveratrol and other nutraceuticals. Ann N Y Acad Sci. (2017) 1403:109–17. doi: 10.1111/nyas.13380, PMID: 28662275
  163. 163 ZhuB XuW LiuJ DingJ ChenX . Osteoinductive agents-incorporated three-dimensional biphasic polymer scaffold for synergistic bone regeneration. ACS Biomater Sci Eng. (2019) 5:986–95. doi: 10.1021/acsbiomaterials.8b01371, PMID: 33405789
  164. 164 ShiGS LiYY LuoYP JinJF SunYX ZhengLZ et al. . Bioactive plga/tricalcium phosphate scaffolds incorporating phytomolecule icaritin developed for calvarial defect repair in rat model. J Orthop Translat. (2020) 24:112–20. doi: 10.1016/j.jot.2020.05.008, PMID: 32775203 PMC7390784
  165. 165 FengQ XuJ ZhangK YaoH ZhengN ZhengL et al. . Dynamic and cell-infiltratable hydrogels as injectable carrier of therapeutic cells and drugs for treating challenging bone defects. ACS Cent Sci. (2019) 5:440–50. doi: 10.1021/acscentsci.8b00764, PMID: 30937371 PMC6439455
  166. 166 GuoYH ZhaoS Du YXQJ ChenBL YuCQ . Effects of ginsenoside rg1-loaded alginate-chitosan microspheres on human bone marrow stromal cells. Biosci Rep. (2017) 37:BSR20160566. doi: 10.1042/BSR20160566, PMID: 28536312 PMC6434175
  167. 167 WanJ MaT JinY QiuS . The effects of morin on bone regeneration to accelerate healing in bone defects in mice. Int J Immunopathol Pharmacol. (2020) 34:1682200157. doi: 10.1177/2058738420962909, PMID: 33035102 PMC7550952
  168. 168 LiuX ChenY ChenX SuJ HuangC . Enhanced efficacy of baicalin-loaded tpgs polymeric micelles against periodontitis. Mater Sci Eng C Mater Biol Appl. (2019) 101:387–95. doi: 10.1016/j.msec.2019.03.103, PMID: 31029332
  169. 169 WangP GuoW HuangG ZhenJ LiY LiT et al. . Berberine-based heterogeneous linear supramolecules neutralized the acute nephrotoxicity of aristolochic acid by the self-assembly strategy. ACS Appl Mater Interf. (2021) 13:32729–42. doi: 10.1021/acsami.1c06968, PMID: 34247476
  170. 170 ZhouY ZhangD ChengH WuJ LiuJ FengW et al. . Repairing gut barrier by traditional chinese medicine: roles of gut microbiota. Front Cell Infect Microbiol. (2024) 14:1389925. doi: 10.3389/fcimb.2024.1389925, PMID: 39027133 PMC11254640

Author Contributions

  • Mingdong Liu: Writing – review & editing, Writing – original draft
  • Jiaqi Gong: Writing – original draft, Writing – review & editing
  • Yaqi Liu: Writing – original draft, Writing – review & editing
  • Jiayao Yu: Writing – original draft, Writing – review & editing
  • Zepeng Hu: Writing – original draft, Writing – review & editing
  • Zheng Liu: Writing – review & editing, Writing – original draft

Declarations

Funding

The author(s) declared that financial support was received for this work and/or its publication. This work was funded by Shaoxing University Enterprise Important Horizontal Topic (No.2024USXH287).

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