Nutrient sensing in intestinal stem cell: Linking dietary nutrients to cellular metabolic regulation

Abstract

Diet and nutrition significantly influence health, largely by regulating intestinal nutrient absorption. The intestinal epithelium, as the primary site for nutrient uptake, undergoes continuous renewal driven by precise regulation of intestinal stem cells (ISCs). Nutrient sensing and metabolism are key determinants of ISC fate, making ISCs a central link between nutrient metabolism and the regulation of intestinal tissue renewal and homeostasis. Understanding how ISCs respond or make adaptations to nutritional signals is therefore vital for maintaining intestinal homeostasis. Recent studies have spotlighted the origin and identity of ISCs and broadened our insight into the plasticity and function of ISCs under different conditions. Mitochondria, the central hubs of energy production and metabolic signals provided by dietary components and metabolic substrates, such as glucose, amino acids, and lipids, govern the intricate balance between self-renewal and differentiation of ISCs. This review highlights the importance of nutrient sensing, metabolic regulation, and mitochondrial function in the specification of ISC fate. A thorough understanding of these mechanisms paves the way for the development of stem cell-based therapy for the mucosal healing of gastrointestinal diseases and diet intervention to foster body health.

Key Words: Intestinal stem cell; Intestinal organoids; Nutrient sensing; Metabolic regulation; Mitochondria

Core Tip: Diet and nutrition play a critical role in health by regulating intestinal nutrient absorption, with intestinal stem cells serving as the central link between nutrient metabolism and intestinal tissue renewal. Nutrient sensing, metabolic regulation, and mitochondrial function are key determinants of intestinal stem cell fate, balancing self-renewal and differentiation. Understanding these mechanisms offers insights into stem cell-based therapies for gastrointestinal diseases and dietary interventions to promote health.

INTRODUCTION

The mammalian intestinal epithelium constitutes the largest mucosal barrier and serves as the primary site for nutrient absorption[1,2]. Dietary components regulate physiological processes by triggering metabolic and sensory signaling pathways directly at the intestinal lining prior to their systemic dissemination. The nutritional microenvironment can influence the differentiation and self-renewal activities of intestinal stem cells (ISCs), which reside at the base of crypts and orchestrate epithelial turnover[3,4]. This adaptive mechanism ensures the maintenance of functional and structural integrity of the intestine under varying nutritional conditions, potentially positioning ISCs as central integrators coupling luminal nutrient sensing with tissue homeostasis.

The proliferation and differentiation of ISCs are tightly regulated by nutritional factors. Macronutrients, including saccharides, lipids, and amino acids, mediate the mitotic expansion of ISCs into transit-amplifying cells through two major signaling pathways: Wnt/β-catenin and Notch. Among these, the Wnt/β-catenin pathway primarily regulates ISCs self-renewal and proliferation, while the Notch pathway governs cell fate determination and differentiation. Following migration from the crypt base toward the intestinal lumen, transit-amplifying cells undergo cell cycle exit and lineage commitment, ultimately differentiating into two principal epithelial lineages: Absorptive cells, primarily enterocytes responsible for nutrient absorption, and secretory cells, including goblet cells, Paneth cells, enteroendocrine cells (EECs), and Tuft cells[3,5]. Notably, ISCs and their differentiated progeny exhibit distinct metabolic profiles throughout their lineage commitment. During differentiation, ISCs alter their metabolic modes [e.g., oxidative phosphorylation (OXPHOS), fatty acid oxidation and glycolysis] through nutrient-sensing pathways regulated by mammalian target of rapamycin, peroxisome proliferator-activated receptor (PPAR), AMP-activated protein kinase and other related signaling[6,7]. If abnormalities in nutrient-sensing pathways occur due to factors such as malnutrition, they may lead to intestinal inflammation and barrier dysfunction[8]. Deciphering the precise regulatory mechanisms through which dietary components modulate ISC plasticity represents a crucial research topic essential for understanding intestinal homeostasis, developing nutritional interventions, and holds translational promise for precision nutrition strategies targeting mucosal regeneration disorders.

This review summarizes the importance of nutrient sensing, metabolic regulation, and mitochondrial function in determining ISC fate and their impact on intestinal health, aiming to elucidate the complex interactions between diet, metabolism, and stem cell biology. By mapping the nutrient sensing-metabolic regulation axis, we lay a theoretical foundation for developing stem cell-based therapeutic strategies for gastrointestinal diseases and innovative dietary interventions to promote intestinal health.

EMERGING INSIGHTS INTO ISC

Previous studies have shown that the crypts harbor two distinct ISC populations: Crypt base columnar (CBC) cells, characterized by high expression of leucine-rich repeat-containing G protein-coupled receptor 5 (Lgr5), which drive constitutive epithelial renewal through active proliferation[9]; and a quiescent population of cells located at the fourth position above the crypt base, characteristically expressing homeodomain only protein, Bmi1, mTert, and leucine-rich repeats and immunoglobulin-like domains containing protein 1, and serves as a reserve regenerative pool activated during mucosal injury[10-14].

Emerging studies challenge the exclusivity of Lgr5+ ISCs in lineage specification, revealing fibrinogen-binding protein 1+ capable of regenerating crypt-villus structures (including Lgr5+ CBC populations) through biphasic regenerative trajectories[15,16]. Single-cell transcriptomic and chromatin accessibility analyses further identified the Lgr4+ proliferative cells within the crypt isthmus (+4 to +13 cell positions from the crypt base). These cells exhibit functional plasticity to replenish Lgr5+ pools post-depletion[17]. Notably, co-expression of fibrinogen-binding protein 1 in Lgr4+ cells implies potential cellular overlap, yet whether these populations represent distinct states, transitional intermediates, or spatially adjacent subsets remains unresolved.

Intestinal repair following injury fundamentally differs from homeostatic renewal by engaging dedifferentiation of specialized cells, which reveal context-dependent stem cell adaptations. Dextran sodium sulfate-induced colitis triggers fetal-like epithelial reprogramming through extracellular matrix remodeling, FAK/Src activation, and YAP/TAZ nuclear translocation[18]. Radiation-resistant tuft cells respond to interleukin (IL)-4/IL-13 signaling by acquiring multipotent differentiation capacity[19], while Bmi1+Prox1+ EECs demonstrate injury-activated stem potential[20]. LY6A (SCA-1) fetal-like stem cells demonstrate organoid-forming capacity and regenerative functionality post-injury[21]. Single-cell analyses further identify clustering rare revival stem cells marked by clustering expression that generate all major intestinal lineages through temporal differentiation hierarchies[22]. Lineage tracing confirms enhanced differentiation potential of LGR5+p27+ cells following 5-fluorouracil-induced injury[23]. These findings reveal that facultative stem cell states following injury are contextually mobilized, yet the molecular logic governing their hierarchical interactions and niche-specific activation thresholds remains incompletely defined.

Despite the identification of diverse subpopulations with regenerative potential, current research on dietary regulation of stem cell fate remains disproportionately focused on LGR5+ ISCs. Future investigations should systematically elucidate how nutrient-sensing pathways and dietary components modulate the context-dependent activation of these heterogeneous regenerative populations, particularly facultative progenitors to unravel their metabolic dependencies and therapeutic potential.

MODULATION OF ISCS BY DIETARY NUTRIENTS

Dietary nutrients have a wide range of effects on health and disease[24]. A deeper understanding of the regulatory relationship of dietary factors on ISCs is not only conducive to further understanding the biological properties of ISCs, but will also strongly contribute to the clinical translation of dietary interventions toward targeting ISCs for the treatment of intestinal diseases (Figure 1).

Figure 1 Schematic overview of key metabolites regulating intestinal stem cells homeostasis. SCFAs: Short-chain fatty acids.

Saccharides and their metabolites

Glucose functions as the primary energetic substrate governing ISC homeostasis, with metabolic plasticity between glycolysis and OXPHOS critically determining ISCs fate. ISCs predominantly rely on glycolytic metabolism to sustain proliferative self-renewal, while metabolic reprogramming toward OXPHOS drives secretory lineage commitment, as demonstrated by impaired differentiation upon OXPHOS inhibition[25]. Pharmacological suppression of glycolysis (e.g., 2-deoxyglucose) or genetic ablation of hexokinase 2, the rate-limiting glycolytic enzyme, robustly attenuates ISC proliferation, confirming their obligate dependence on glycolytic flux[26,27]. Paradoxically, chronic hyperglycemia disrupts ISC homeostasis through metabolic stress overload. In Drosophila models, high-sugar diets induce ISC dysfunction via oxidative stress-mediated activation of the c-Jun N-terminal kinase pathway and suppression of regenerative Janus kinase-signal transducer of activation (STAT) signaling, collectively skewing ISC fate toward premature differentiation and depleting the stem cell pool[28,29]. These findings underscore the necessity for precise regulation of glycolytic activity to balance ISC self-renewal with lineage specification, revealing glucose as both a metabolic substrate and a critical modulator of stem cell plasticity.

Pyruvate, a key metabolic node generated from glucose via glycolysis in the cytoplasm, regulates ISC fate. Impaired function of the mitochondrial pyruvate carrier (MPC) disrupts mitochondrial pyruvate import, enhancing ISC self-renewal, amplifying stemness-associated transcriptional networks, and promoting proliferation, while MPC overexpression suppresses ISC expansion, establishing MPC as a bidirectional rheostat of stem cell dynamics[30-32]. Interestingly, terminally differentiated intestinal epithelial cells can regulate ISCs activity, as MPC deficiency in epithelial cells non-autonomously stimulates ISC proliferation[33]. A recent breakthrough study has structurally revealed the molecular architecture of MPC, substrate recognition motifs, transmembrane translocation pathway, and pharmacological inhibition mechanisms[34]. These structural insights have laid a foundation for developing MPC-targeted therapeutics to modulate ISCs functionality.

Lactate, the terminal glycolytic metabolite, serves dual roles as both a metabolic substrate (via pyruvate conversion for OXPHOS) and a signaling molecule in ISCs. Paneth cell-derived lactate sustains elevated ISC OXPHOS via mitochondrial substrate channeling, where reactive oxygen species (ROS) hormesis activates p38 mitogen-activated protein kinases (MAPK)-mediated morphogenic programs essential for crypt-villus patterning activity, which paradoxically avoids oxidative damage through controlled ROS generation. Mechanistically, this redox balance activates p38 MAPK-mediated differentiation programs essential for crypt-villus axis formation[35]. Furthermore, lactogenic probiotics (Bifidobacterium, Lactobacillus) enhance ISC proliferation and mucosal repair regeneration via Gi-protein-coupled receptor 81 (GPR81)-dependent coordination of Wnt3 secretion from co-activation in Paneth cells and stromal niches, driving β-catenin-mediated regeneration in chemotherapy/radiation injury models[36]. Notably, Lactobacillus amylovorus specifically potentiates ISC function through this lactate-GPR81-Wnt/β-catenin axis, suggesting strain-specific therapeutic applications for mucosal homeostasis[37]. Histone lactylation - a lactate-derived epigenetic modification - regulates stemness in other stem systems[38,39], yet its role in ISCs remains unstudied, pointing to an unexplored gap in metabolic-epigenetic crosstalk during intestinal repair regeneration. Numerous lactic acid-producing bacterial strains have been documented to enhance gut health, and the specific species and their applications are summarized in Table 1[36,37,40-48]. Future research should focus on determining whether the health-promoting effects of these bacterial strains across multiple human physiological systems are exclusively mediated by lactic acid, while exploring the potential of developing dietary strategies involving lactic acid supplementation as alternatives to probiotic interventions for optimizing ISC functionality (Table 1).

Table 1 Functional characteristics of lactic acid-producing bacterial strains in modulating intestinal homeostasis.

Bacterial strains	Mechanism/pathway	Biological effects	Ref.
Bifidobacterium spp.	GPR81 signaling	Promoting ISCs proliferation	[36]
Lactobacillus amylovorus	GPR81-Wnt/β-catenin axis	Enhancing ISCs proliferation	[37]
Lactobacillus salivarius	SUCNR1-mitochondria axis	Activating ISCs activity	[40]
Lactobacillus paracasei VL8	Tryptophan microbial metabolism	Inducing ISCs differentiation	[41]
Lactobacillus delbrueckii	-	Expanding ISCs population	[42]
Lactobacillus rhamnosus, Lactobacillus acidophilus, Bifidobacterium lactis	-	Augmenting innate and adaptive immunity	[43]
Lactobacillus casei	-	Ameliorating intestinal injury	[44]
Lactobacillus reuteri	Wnt/β-catenin axis	Mitigating intestinal mucosal damage	[45]
Lactipianibacillus plantarum	-	Alleviating constipation	[46]
Lactipianibacillus plantarum HFY11	-	Suppressing colitis	[47]
Lacticaseibacillus paracasei JY06E, Lactobacillus gasseri JM1	-	Relieving constipation	[48]

GPR81: Gi-protein-coupled receptor 81; ISCs: Intestinal stem cells; SUCNR1: Succinate receptor 1.

L-fucose, a dietary monosaccharide with therapeutic potential for intestinal disorders, mediates mucosal repair through multi-layered mechanisms[49,50]. L-fucose regulates the unfolded protein response by direct fucosylation of ISCs to defend against inflammatory injury[51]. Concurrently, L-fucose enriches Akkermansia-derived propionate biosynthesis to indirectly drive ISC proliferation[52]. In addition, L-fucose activates the aryl hydrocarbon receptor (AHR)/IL-22 axis in lamina propria monocytes, establishing an immune-metabolic niche that promotes ISC self-renewal through paracrine signaling[53]. L-fucose orchestrates intestinal homeostasis through coordinated mechanisms involving ISCs fucosylation modification, microbial metabolite crosstalk, and immune niche modulation, reflecting its systemic regulatory capacity across biological compartments.

Dietary carbohydrates and their metabolites exert pleiotropic control over ISC fate, including energy metabolism reprogramming, epigenetic regulation, post-translational modifications, and symbiotic microbiota crosstalk. Importantly, moderate carbohydrate intake, strategic lactate supplementation, and consumption of beneficial dietary monosaccharides may enhance ISC-mediated epithelial regeneration and intestinal homeostasis by optimizing metabolic flexibility.

Lipids and their metabolites

High-fat diet (HFD) induces aberrant ISC hyperproliferation, thereby accelerating colorectal tumorigenesis and metabolic syndrome. Mechanistically, HFD enhances the proliferative capacity of LGR5+ ISCs through PPARδ activation, which directly links dietary lipid overload to oncogenic transformation[7]. This synergizes with HFD-induced de novo lipogenesis and convergent PPAR/insulin-like growth factor-1R-protein kinase B (AKT) signaling, which result in dysregulated ISC expansion. The resultant mucosal hyperplasia and metabolic dysfunction establish a pathogenic feedforward loop that amplifies carcinogenic and metabolic derangements[32].

Fatty acids play indispensable roles in ISC maintenance. Hepatic nuclear factors hepatocyte nuclear factor 4 alpha and hepatocyte nuclear factor 4 gamma orchestrate fatty acid β-oxidation gene networks essential for ISC self-renewal[54]. Ceramides, sphingolipid derivatives generated via serine palmitoyltransferase-mediated biosynthesis, act as pro-stemness signals by activating PPARα and fatty acid binding protein 1. This ceramide-PPARα axis enhances lipid utilization and intestinal progenitor proliferation, with sphingolipid biosynthetic enzymes (including serine palmitoyltransferase) upregulated in human intestinal adenomas, underscoring their conserved role in tumorigenesis[55].

Ketone bodies are of significance as intermediates in the oxidation of fatty acids, and have emerged as important regulators of ISC functionality. The ketogenic diet, a high-fat, low-carbohydrate regimen mimicking fasting metabolism, induces ketogenesis via hepatic and intestinal 3-hydroxy-3-methylglutaryl-CoA synthase 2. 3-hydroxy-3-methylglutaryl-CoA synthase 2 is highly expressed in Lgr5+ ISCs, and its genetic ablation impairs intestinal stemness and regenerative capacity. Mechanistically, β-hydroxybutyrate, a predominant ketone body, enhances ISC post-injury regeneration through histone deacetylase (HDAC) inhibition-mediated to stimulate Notch activation[56]. Furthermore, β-hydroxybutyrate supplementation has been demonstrated to suppress colorectal tumorigenesis[57]. These findings suggest that targeted metabolite supplementation may circumvent the need for complex dietary interventions, offering a dual therapeutic strategy to enhance ISC functionality while inhibiting oncogenic progression.

These findings collectively delineate a dynamic lipid-metabolic network wherein PPAR isoforms (δ/α) and ketone body signaling serve as central nodes integrating dietary inputs, β-oxidation, and sphingolipid metabolism to balance ISC self-renewal, differentiation, and oncogenic risk. The convergence of HFD- and ketogenic diet-mediated effects on ISC plasticity underscores the profound influence of lipid metabolism on epithelial regeneration and disease susceptibility. While lipid metabolites enhance ISC proliferation, their therapeutic application remains limited due to oncogenic risks and metabolic comorbidities. Future research must delineate context-specific mechanisms to safely harness fatty acids for ISC expansion.

Amino acids

Rapid renewal of the intestinal epithelium, a process demanding substantial amino acids for protein synthesis, is tightly regulated by specific amino acids that orchestrate ISC functionality through conserved metabolic and signaling networks.

Glutamine enhances ISC-mediated regeneration by amplifying Wnt/β-catenin signaling in a dose-dependent manner, while fueling glutaminolysis-dependent energy metabolism[58,59]. Glutamate (Glu), the most abundant amino acid in luminal proteins, modulates calcium signaling to adapt ISC proliferation and differentiation rates to dietary fluctuations in Drosophila[60]. While in porcine models, extracellular Glu was utilized to activate mechanistic target of rapamycin complex 1 (mTORC1) via insulin receptor/insulin receptor substrates/phosphatidylinositol-3-kinase/Akt, epidermal growth factor receptor/extracellular signal-regulated kinase, and further β-catenin/frizzled7 pathways, synergistically driving epithelial renewal[61-63]. Asparagine, a conditionally non-essential amino acid, maintains intestinal homeostasis by suppressing senescent ISC hyperproliferation via autophagy activation[64].

L-arginine stimulates ISC proliferation through dual niche signaling: Wnt2b derived from CD90+ stromal cells and Wnt3a derived from Paneth cells are both critical for epithelial barrier integrity[65,66]. Methionine reactivates Wnt/β-catenin signaling through metabolic-epigenetic crosstalk, potentiating ISC self-renewal[67]. Evolutionarily conserved Sestrins emerge as central nutrient sensors, suppressing target of rapamycin complex 1 and augmenting autophagy to fine-tune ISC turnover. Sestrin overexpression extends intestinal longevity by balancing anabolic and catabolic processes under dietary amino acid fluctuations[68].

Collectively, amino acids coordinate ISC dynamics through interconnected pathways encompassing Wnt/β-catenin, mTORC1, and autophagy, to align epithelial renewal with metabolic demands. Glutamine/Glu drive proliferative outputs and asparagine/Sestrin enforce quality control via proteostatic mechanisms. L-arginine/methionine fine-tune niche signaling to sustain stemness. Future therapeutic strategies may focus on modulating amino acid availability in ISCs through dietary interventions or targeted regulation of endogenous metabolic pathways, contingent upon precise characterization of amino acid-specific impacts on ISC fate determination.

Gut microbiota and their metabolites

The gut microbiota, a complex ecosystem, critically regulates ISCs dynamics through intertwined immune and metabolic pathways to sustain epithelial homeostasis and host health[69,70]. Gut microbiota-derived components orchestrate ISC-immune crosstalk through pattern recognition receptor activation. For instance, Lactobacillus rhamnosus GG stimulates Toll-like receptor 2 on macrophages via lipoteichoic acid, inducing chemokine secretion and migration of prostaglandin E2-producing mesenchymal ISCs to shield ISCs from radiation-induced damage[71]. Crypt-specific microbiota-derived lipopolysaccharide maintains the proliferation-differentiation balance of colonic epithelium[72], while muramyl dipeptide, a conserved peptidoglycan motif, activates nucleotide-binding oligomerization domain 2 (NOD2) enriched in LGR5+ ISCs to enhance ROS clearance via autophagy-related gene 16 L1/NOD2-dependent mitophagy to mitigates oxidative stress-induced apoptosis[73,74].

Microbial metabolites exert compartmentalized control over ISCs dynamics. Short-chain fatty acids, produced via anaerobic fermentation of dietary fibers, act as ligands for G-protein-coupled receptors and HDAC inhibitors. Acetate supports organoid growth by suppressing β-oxidation under low acetyl-CoA conditions[75], while propionate restores Lgr5+ ISCs in dextran sodium sulfate-injured organoids via GPR41/GPR43-dependent signaling[52,76]. Of note, butyrate exhibits dual roles: It preserves Lgr5+ ISC stemness through HDAC inhibition[77], yet suppresses ISCs proliferation via forkhead box O3 activation at physiological concentrations[78].

Tryptophan metabolism bridges microbiota-ISC crosstalk through divergent signaling axes. Lactobacillus murinus-derived indole-3-acetic acid converted from tryptophan suppresses ISC differentiation via mitochondrial bioenergetics disruption[79], while indole-3-aldehyde activates group 3 innate lymphoid cells via AHR to secrete IL-22, promoting ISC proliferation through STAT3 signaling[80]. Host-derived serotonin, regulated by microbiota metabolites like valeric acid, enhances prostaglandin E2 production in macrophages via 5-HT(2A) serotonin receptor/5-HT(3A) serotonin receptor receptors, activating Wnt/β-catenin signaling in ISCs to drive self-renewal[81].

The gut microbiota as a metabolic-immune nexus, integrating microbial ligands (e.g., muramyl dipeptide, short-chain fatty acids) and host pathways (Toll-like receptor 2/NOD2, AHR/STAT3) to balance ISC proliferation, differentiation, and stress adaptation. Future therapeutic strategies targeting microbiota-derived metabolites or immune signaling of ISCs niche could restore epithelial integrity in inflammatory bowel disease, radiation injury, and metabolic disorders.

Fasting

Research has shown that various fasting strategies can significantly extend the lifespan of different organisms and enhance their tissue regenerative capabilities[82-84]. Under caloric restriction (a 40% reduction in caloric intake), the signaling of mTORC1 in Paneth cells is suppressed, leading to an increase in the expression of bone marrow stromal cell antigen-1[85]. Bone marrow stromal cell antigen-1 is an ectoenzyme that generates the paracrine factor cyclic ADP ribose, which effectively enhances the self-renewal capacity of ISCs[86]. Short-term activation of mTORC1 signaling aids in the physiological regulation of ISCs, whereas sustained mTORC1 signaling may impair ISCs function[87,88]. Therefore, by rationally modulating this mechanism - such as through controlled caloric restriction or the use of drugs like rapamycin and cyclic ADP ribose - it may become a potential strategy for improving ISCs function and treating related diseases.

It has been reported that short-term fasting (24-hour) enhances ISC function via fatty acid oxidation activation[89]. Unlike caloric restriction, short-term fasting-refeeding cycles enhance ISCs function primarily mediated by refeeding-induced activation of phosphatidylinositol-3-kinase/AKT/mTORC1 signaling and the promotion of global protein translation, which is independent of the Paneth cell niche[90]. However, this diet may also lead to increased polyamine metabolism and protein synthesis, thereby elevating the risk of tumor formation[91]. Given the different effects of fasting and fasting-refeeding on ISCs function and carcinogenesis, future studies are needed to further clarify the roles of fasting-feeding timing, total calorie intake, and meal content during refeeding, as well as whether repetitive cycles of fasting and refeeding (such as asynchronous intermittent fasting regimens, e.g., 2-day fasting per week) play significant roles in fasting-related ISCs regulation and carcinogenesis. These investigations will facilitate the development of optimized fasting-refeeding strategies for tissue regeneration that do not elevate cancer risk.

Others

There are other factors that can influence the functional state of ISCs. Bile acids, not only participate in lipid digestion[92], but also act as pleiotropic signaling modulators to regulate physiological responses[93]. The release of endogenous bile acids activates the Takeda G protein-coupled receptor 5 receptor in ISCs, which supports ISC self-renewal by activating the SRC/YAP regeneration mechanism[94].

Trace elements such as iron also impact ISCs fate determination. Iron overload can inhibit the proliferation of ISCs by suppressing the Notch signaling pathway[95,96], promoting their differentiation into secretory mature cells while inhibiting absorptive lineages[97]. In addition, iron overload may lead to ferroptosis in the intestinal epithelium[98]. These findings point to the multifactorial regulatory framework governing ISC behavior. Further exploration of undiscovered modulators and their mechanistic interplay will advance our understanding of intestinal regeneration (Figure 2).

Figure 2 Dietary nutrients can regulate self-renewal and differentiation capacities of intestinal stem cells. A: Glucose balances intestinal stem cell (ISC) proliferation/differentiation via glycolytic pyruvate-trichloroacetic acid-oxidative phosphorylation-reactive oxygen species-p38 axis. Lactate fuels ISC energy needs through autocrine metabolism, while concurrently stimulating Paneth cell-derived Wnt3 via Gi-protein-coupled receptor 81 to activate Wnt/β-catenin. L-fucose maintains stemness through alpha1,2-fucosylation of N-acyl sphingosine amidohydrolase 2; B: High-fat diet activates PPAR δ to enhance leucine-rich repeat-containing G protein-coupled receptor 5+ ISC proliferation. Serine palmitoyltransferase-derived ceramides activate PPAR α/fatty acid binding protein 1 stemness signaling, while hepatocyte nuclear factor 4 alpha/hepatocyte nuclear factor 4 gamma regulate fatty acid β-oxidation for self-renewal; C: Glutamine/L-arginine/methionine/glutamate /asparagine modulate ISC stemness via Wnt/β-catenin signaling. GPR81: Gi-protein-coupled receptor 81; HK2: Hexokinase 2; MPC: Mesenchymal progenitor cell; TCA: Trichloroacetic acid; OXPHOS: Oxidative phosphorylation; ROS: Reactive oxygen species; MAPK: Mitogen-activated protein kinases; ASAH2: Alpha1,2-fucosylation of N-acyl sphingosine amidohydrolase 2; FA: Fatty acid; PPAR: Peroxisome proliferator-activated receptor; Fabp1: Fatty acid binding protein 1; SPT: Serine palmitoyltransferase; HNF4A: Hepatocyte nuclear factor 4 alpha; HNF4G: Hepatocyte nuclear factor 4 gamma; FAO: Fatty acid β-oxidation; HMGCS2: 3-hydroxy-3-methylglutaryl-CoA synthase 2; βOHB: Beta-hydroxybutyrate; HDAC: Histone deacetylase; Arg: L-arginine; Asn: Asparagine; MAPK: Mitogen-activated protein kinases; IR: Insulin receptor; IRS: Insulin receptor substrates; PI3K: Phosphatidylinositol-3-kinase; Akt: Protein kinase B; EGFR: Epidermal growth factor receptor; ERK: Extracellular signal-regulated kinase; Glu: Glutamate; Gln: Glutamine; Met: Methionine.

MITOCHONDRIA AND ISCS

Mitochondria serve as central bioenergetic and biosynthetic hubs in ISCs, fueling ISC function and epithelial renewal[99]. The synthesis of amino acids[100], nucleotides, and lipids[101] depends on mitochondria to meet cellular biosynthetic demands. Moreover, mitochondrial dynamics can regulate the differentiation of ISCs and maintain the structural and morphological integrity of mitochondria[102]. ISCs exhibit metabolic heterogeneity based on functional states: Quiescent ISCs exhibit lower energy consumption with fewer mitochondria. While activated Lgr5+ CBCs undergo mitochondrial biogenesis and morphological elongation to adopt OXPHOS-dominant metabolism, meeting heightened biosynthetic demands[35]. This metabolic flexibility enables ISCs to dynamically adjust their metabolic patterns and mitochondrial dynamics in response to physiological demands[30,103,104].

Changes in metabolic patterns, such as during the differentiation of ISCs into Paneth cells, are accompanied by downregulation of forkhead box O3/Notch signaling and a shift toward glycolysis for energy production[105]. Additionally, alterations in the niche can influence the metabolic mode of ISCs. For example, EECs depletion triggers fatty acid β-oxidation activation to sustain ATP production and stemness maintenance[54,106]. Mitochondria-derived ROS, long considered byproducts of respiration exhibit biphasic regulation[107,108]: Physiological ROS levels activate p38/MAPK-mediated Lgr5+ CBC self-renewal[35,109], whereas excessive ROS leads to oxidative stress to impair cellular function or mitophagy-dependent mitochondrial quality control to preserve ISC integrity[74] (Figure 3).

Figure 3 Distinct regulatory effects of mitochondrial reactive oxygen species levels on intestinal stem cells fate. A: Physiological levels of mitochondrial reactive oxygen species modulate mitochondrial dynamics and quality control mechanisms to coordinate intestinal stem cell self-renewal and differentiation; B: Excessive mitochondrial reactive oxygen species accumulation triggers intestinal stem cell death. ROS: Reactive oxygen species; mtROS: Mitochondrial reactive oxygen species; Drp1: Dynamin-related protein 1; MFF1: Mitochondrial fission factor 1; Fis1: Fission 1; Pink1: Phosphatase and tensin homolog-induced putative kinase 1; Atg: Autophagy-related gene; OPA1: Optic atrophy 1; MFN2: Mitofusin-2.

Mitochondrial dysfunction emerges as a pathogenic nexus across intestinal pathologies, where impaired bioenergetics and redox imbalance converge to disrupt epithelial homeostasis[110-112]. During the development of colorectal tumors, aerobic glycolysis in ISCs is enhanced, accompanied by weakened OXPHOS[31], and abnormal pyruvate metabolism[113]. Ulcerative colitis manifests mitochondrial electron transport chain defects that drive pathogenic ROS cascades[114,115], while fucosyltransferase 2-deficient ISCs can impair respiratory chain complexes and mitophagy, compromising ISCs function[116]. As the hub and energy factory of metabolism, in-depth research into mitochondrial function will provide critical insights into further elucidating the metabolic regulation mechanisms of ISCs.

APPLICATIONS OF INTESTINAL ORGANOIDS

Stem cells have demonstrated vast potential in regenerative medicine, with nutritional status playing a crucial regulatory role in these processes. The stem cell niche is a highly specialized and dynamic microenvironment surrounding ISCs[117], which not only provides structural support but also regulates stem cell behavior through signaling mediated by environmental nutrients[118,119]. Human intestinal organoids transcend 2D culture limitations by recapitulating crypt-villus architectures and niche interactions[120,121]. By adjusting the nutrient composition of the culture medium, the effects of nutrition on ISCs behavior can be easily manifested.

Multiple gastrointestinal organoid platforms are being utilized for high-throughput drug and nutrient screening. Notably, jejunal organoid-derived monolayers permit direct quantification of nutrient and electrolyte absorption, highlighting the potential utility of organoid models in nutritional screening[122-124]. Studies have demonstrated that multi-phenotypic screening, using miniaturized organoid models and single-cell RNA sequencing, can identify small molecules that regulate ISC differentiation[125]. These methods can also be applied to screen for nutrients or factors with the potential to modulate stem cell differentiation. Microfluidic organoids have recently been utilized for drug screening or fundamental research[126]. In the future, large-scale screening may uncover novel nutrients or metabolites and reveal their regulatory mechanisms on stem cell behavior. As organoid technology continues to advance and find broader applications, it is expected to uncover additional unknown nutritional factors that regulate ISC behavior, and engineer personalized nutritional matrices for regenerative therapies.

CONCLUSION

Intestinal epithelial regeneration is governed by ISCs, whose self-renewal and differentiation are dynamically regulated by niche signals, dietary nutrients, and metabolic adaptations. This review highlights how glucose, lipids, amino acids, and microbial metabolites modulate ISC fate via pathways such as glycolysis-OXPHOS transitions, PPAR signaling, and Wnt/β-catenin activation. Mitochondrial dynamics integrate energy production, redox balance, and biosynthesis to sustain stemness, while dietary interventions and microbiota-derived metabolites fine-tune regenerative plasticity. We still do not fully understand the metabolic dependency mechanisms of facultative progenitors or whether they increase cancer risk in specific environments. Advancing organoid-based nutrient screening and resultant therapies may unlock precision strategies to enhance mucosal repair while circumventing metabolic trade-offs in gastrointestinal pathologies.