Natural bioactive compounds in estrogen deficiency-induced osteoporosis: Classification and an integrated gut microbiota-metabolite-immune-bone framework

Table 1 Microbiota-dependent classification of natural bioactive compounds in estrogen deficiency-induced osteoporosis

Category	Representative compounds or interventions	Microbiota dependency	Major gut-derived mediators	Dominant bone-related mechanisms	Evidence level	Ref.
Phytoestrogens and estrogen-like compounds	Puerarin, genistein, daidzein, S-equol, calycosin, 8-prenylnaringenin	Mixed: Direct estrogen receptor modulation plus microbial biotransformation	S-equol, SCFAs, estrobilome-related β-glucuronidase/sulfatase activity	ERα/ERβ signaling, reduced osteoclastogenesis, associated with greater intestinal barrier integrity, decreased systemic inflammation	Moderate preclinical evidence; limited human intervention evidence	[15,24,25,27-29]
Polyphenols, flavonoids, and terpenoids	Flavan-3-ols, ginkgolide B, taraxasterol, Moringa oleifera leaf constituents, quercetin, resveratrol, curcumin	Moderate to high; many compounds require microbial metabolism or reshape microbiota	Phenolic metabolites, SCFAs, altered bile acid and indole metabolites	Antioxidant and anti-inflammatory effects, RANKL/OPG regulation, NF-κB/NFATc1 suppression, MAPK and NLRP3 modulation	Moderate preclinical evidence; mostly OVX animal studies with 16S/metabolomicsevidence	[11,12,30-33]
Polysaccharides, oligosaccharides, and dietary fibers	Dendrobium officinale polysaccharides, Polygonatum polysaccharides, algal oligosaccharides, dietary fiber-rich foods	High; generally act as prebiotic substrates rather than directly absorbed bone-active molecules	Butyrate, acetate, propionate, isovalerate, SCFA-producing bacteria	Enhanced tight junction proteins, Treg induction, reduced inflammation, Wnt/β-catenin activation, improved osteoblastogenesis	Moderate to high when FMT or metabolite evidence is included	[16,35,49,51]
Probiotics, postbiotics, and defined bacterial strains	Lactobacillus rhamnosus GG, Lactobacillus acidophilus, Lactobacillus sakei CVL-001, Parabacteroides distasonis, Clostridium sporogenes	Direct microbiota- targeted intervention	Butyrate, indole propionic acid, bacterial components, TLR2/GPCR-related signals	Th17/Treg rebalancing, reduced IL-17/TNF-α, improved gut barrier, suppressed RANKL-induced osteoclastogenesis	Moderate preclinical evidence; limited evidence for clinical skeletal efficacy	[13,36-40]
Fermented foods and dietary-pattern interventions	Fermented soybeans, Bacillus subtilis-rich foods, quinoa, tryptophan-restricted intermittent diet	High; effects depend on dietary substratesand microbialecological remodeling	Biotin, SCFAs, soyisoflavone metabolites, altered tryptophan metabolites	Improved BMD and trabecular microarchitecture, reduced M1 macrophage polarization, induced osteoclast apoptosis, improved metabolic status	Preliminary-to-moderate preclinical evidence	[35,42,43]
Complex herbal formulations and natural extracts	Roucongrong Pill, Jiaru fuling traditional Chinese medicine formulas, deer velvet antler protein extract	Variable; often multi-component and multi-pathway	SCFAs, steroid-related metabolites, taurine/hypotaurine metabolites, lipid and nucleotide metabolites	Multi-target regulation of gut microbiota, immune balance, steroid hormone biosynthesis, osteoclast inhibition, osteoblast support	Preliminary or hypothesis-generating evidence; causal attribution remains insufficient	[14,34,44,45]

Interventions were classified according to their predominant gut microbiota-dependent effects and bone-related mechanisms. Evidence levels were qualitatively assessed based on available in vitro, animal, and human studies; categories may overlap. SCFAs: Short-chain fatty acids; OVX: Ovariectomy; FMT: Fecal microbiota transplantation; BMD: Bone mineral density; ER: Estrogen receptor.

Table 2 Mechanistic modules linking natural bioactive compounds, gut microbiota, and bone remodeling

Mechanistic module	Upstream trigger or intervention	Key microbial or metabolic mediators	Immune/endocrine/cellular pathway	Skeletal consequence	Main uncertainty	Ref.
Gut barrier-bone module	Estrogen deficiency, dysbiosis, natural compound intervention	LPS, microbial-associated molecular patterns, tight junction proteins	TLR4/NF-κB activation, systemic inflammation, TNF-α and IL-6 release	Increased osteoclastogenesis when barrier is impaired; bone protection when barrier is restored	Whether barrier repair is primary or secondary to microbiota remodeling	[8,15,16,32,36-38]
SCFA-mediated immune-bone module	Prebiotics, polysaccharides, probiotics, fiber-rich diets	Butyrate, acetate, propionate, SCFA-producing bacteria	FFAR2/3 signaling, Treg induction, reduced Th17 response, Wnt/β-catenin activation	Reduced bone resorption and enhanced bone formation	Optimal SCFA profile, dose, and target cell specificity remain unclear	[16,37,38,49,51]
Tryptophan-indole metabolite module	Tryptophan metabolism, defined bacteria, dietary restriction	IPA, IAA, IA, biotin-associated microbial changes	PXR/P65, AhR/NF-κB, AKT/NFATc1/ROS, M1 macrophage polarization, osteoclast apoptosis	Suppressed osteoclast formation and improved trabecular bone microarchitecture	Context-dependent effects of tryptophan restriction and indole metabolites need clarification	[40,43,46,47]
Bile acid-bonemodule	Natural compounds, estrogen deficiency, gut microbiota remodeling	Primary and secondarybile acids, DCA, TGR5-related signals	TGR5/NF-κB, BMSC differentiation, inflammation regulation	Reduced inflammatory bone loss and improved bone remodeling	Human relevance and bile acid subtype-specific effects remain insufficiently defined	[29,49]
Estrobolome-phytoestrogen module	Menopause, phytoestrogen intake, long-term medication	β-glucuronidase/sulfatase activity, S-equol, estrogen recycling metabolites	ERβ signaling, estrogenavailability, intestinal deconjugation, enterohepatic circulation	Potential preservation of bone mass and reduction of bone turnover	Equol-producer status and medication-induced estrobolome changes are under-tested clinically	[24,27,28,41]
TMAO-PERK/mitochondrial stressmodule	Choline/carnitine metabolism, dysbiosis, TMAO exposure	TMAO, TMA-producing bacteria, FMO3 activity	PERK/ATF4/ATF5, ER stress, mitochondrial unfolded protein response, osteoblast proteostasis	Either bone damage or protection depending on dose, source, and metabolic context	Direction of effect is contradictory and likely context-dependent	[48,53]
miRNA/extracellular vesicle module	Gut dysbiosis, natural bioactive compounds, microbial metabolites	Host fecal miRNAs, BMSC-derived exosomal miRNAs, circulating EV-miRNAs	Post-transcriptional regulation of osteogenesis, adipogenesis, immune polarization, and osteoclastogenesis	Potential bridge between microbial signals and bone marrow cell fate	Still emerging; causal links in natural compound studies are largely missing	[17-23,54]

SCFAs: Short-chain fatty acids; IPA: Indole-3-propionic acid; IA: Indoleacrylic acid; IAA: Indole-3-acetic acid; LPS: Lipopolysaccharide.

Table 3 Evidence strength, limitations, and future directions for natural bioactive compounds targeting the gut-bone axis

Evidence category	What is currently supported	Representative examples	Main limitations	Recommended future direction	Translational value
Human intervention and observational evidence	Gut microbiota, metabolites, phytoestrogens, and selected natural products are associated with BMD or bone turnover markers	8-prenylnaringenin trial, PMOP gut microbiota/metabolite studies, breast metabolomics, menopause microbiota studies	Small sample size, short duration, heterogeneous baseline microbiota, limited fracture endpoints	Microbiome-stratified RCTs with BMD, bone turnover, bone quality, and fracture- related outcomes	Limited and heterogeneous human evidence; clinical efficacy remains unestablished
Strong causal animal evidence	Microbiota can mediate or transfer osteoprotective effects	DOP-FMT model, OVX- induced intestinal T cell trafficking, defined bacteria/metabolite studies	Mainly rodent-based; translational relevance to human menopause remains uncertain	Combine FMT, antibiotics, gnotobiotic models, metabolite rescue, and receptor blockade	Mechanistic relevance in experimental models; human translation remains uncertain
Probiotic and defined strain evidence	Specific strains can improve bone loss through immune and barrier regulation	LGG, Lactobacillus acidophilus, Lactobacillus sakei, Parabacteroides distasonis, Clostridium sporogenes	Strain specificity, colonization stability, dose, duration, and long-term safety unclear	Define strain-level metabolic outputs and host-response phenotypes	Potential for clinical investigation; strain-specific efficacy and safety require validation
Natural compound + OVX + 16S/metabolomics evidence	Many natural compounds improve bone parameters and reshape microbiota	Puerarin, quinoa, Moringa oleifera, ginkgolide B, taraxasterol, flavan-3-ols	Often correlation-based; limited causal validation	Add antibiotic depletion, FMT, metabolite supplementation, and pathway inhibition	Preliminary-to-moderate preclinical support; causal validation is needed
Complex herbal formulation and network pharmacology evidence	Multi-component interventions may regulate microbiota, metabolites, endocrine signals, and bone pathways	Roucongrong Pill, traditional Chinese medicine formulas, Jiaru fuling	Active components and key causal nodes are difficult to identify; docking does not prove mechanism	Use component deconstruction, key metabolite validation, and modular causal testing	Exploratory potential; causal attribution and active-component validation remain limited
miRNA and extracellular vesicle evidence	miRNAs may mediate microbiota-host and BMSC-bone communication	Fecal miRNA regulation of microbiota, BMSC exosomal miRNAs, circulating bone-related miRNAs	Few studies directly connect natural compounds, microbiota, EV-miRNAs, and bone outcomes	Integrate fecal/serum/BMSC EV-miRNA sequencing with metabolomics and bone phenotyping	Emerging research direction; currently hypothesis-generating

RCT: Randomized controlled trial; BMD: Bone mineral density; OVX: Ovariectomy; FMT: Fecal microbiota transplantation.