Intestinal stem cell were first characterized by Cheng and Leblond (1974), identifying slender cells scattered among Paneth cells at the crypt base. These cells showed continuous cell flow from crypt to villi but not definitively proven as stem cells. Later studies confirmed the presence of stem and progenitor cells through short-lived and long-lived clones (Bjerknes and Cheng, 1999; Winton et al., 1988). LGR5+ was identified as an active stem cell marker at crypt base, while Bmi1 marks quiescent stem cells at the “+4” position (Barker et al., 2007; Potten et al., 2002). Under normal circumstances, LGR5+ cells divide rapidly for epithelial renewal (Bloemendaal et al., 2016), while “+4” position cells activated during stress to replace damaged intestinal cells (Montgomery et al., 2011; Takeda et al., 2011). The crypt balances these cell types for self-renewal and repair (Li and Clevers, 2010). Stem cells activity is regulated by multiple signaling pathways (Hou et al., 2017). WNT3, mainly produced by Paneth cells, is essential (Farin et al., 2016), with R-spondin-1 enhancing WNT signaling (Koo et al., 2012; Yan et al., 2017). Notch and BMP signaling also contribute to their proper self-renewal and differentiation (He et al., 2004).

Paneth cells are specialized secretory cells located at the base of small intestinal crypts, interspersed among intestinal stem cells. They are characterized by large eosinophilic secretory granules containing multiple antimicrobial components such as defensins and lysozyme, which are released into the intestinal lumen to support the mucosal barrier (Clevers and Bevins, 2013). Paneth cells also play a key role in maintaining the intestinal stem cell niche (Sato et al., 2011; Clevers, 2013). They achieve this by secreting key signaling molecules such as WNT3, epidermal growth factor (EGF), and Notch ligands, which promote the proliferation and differentiation of LGR5+ stem cell. Genetic ablation of Paneth cells in mice leads to the loss of LGR5+ stem cells, highlighting their essential role in supporting the stem cell niche (Geiser et al., 2012). Abnormalities in Paneth cells are associated with many human disease processes, including Crohn's disease and graft-vs.-host disease (Eriguchi et al., 2012). WNT signaling drives Paneth cell maturation and migration to the base of the small intestinal crypts. In contrast, Notch signaling inhibits their development by suppressing ATOH1, which is critical for secretory cell differentiation (Batlle et al., 2002; Shroyer et al., 2007).

Intestinal goblet cells are scattered among absorptive cells in the intestinal epithelium. They are characterized by a narrow cytoplasmic base and an expanded apical region filled with mucin-containing secretory granules, giving them a goblet-like appearance. These cells produce mucins, which combine with water to form mucus, creating a protective and lubricating intestinal barrier. Mucin genes are mainly divided into secreted and membrane-bound types (Dekker et al., 2002; Birchenough et al., 2015), with MUC2 being the most studied, forming a protective mucus layer (van der Post et al., 2019). Goblet cells also secrete factors like trefoil factor 3 (TFF3), which promote epithelial repair by enhancing cell migration and survival during injury (Taupin et al., 2000). In addition, goblet cells may contribute to gut homeostasis by releasing other bioactive molecules, such as antimicrobial peptides and cytokines. Their differentiation is regulated by inhibition of WNT and Notch signaling pathways.

Tuft cells are chemosensory sentinel cells in organs such as the intestine and lungs, responding to stimuli such as hypoxia and infection (Schneider et al., 2019). They modulate mucosal immunity through G protein-coupled receptors (e.g., taste receptors). Following helminth infection and allergen deposition, the number of tuft cells and goblet cells increases rapidly. This expansion is driven by IL-4 and IL-13 secreted by type 2 innate lymphoid cells (ILC2s), which act through the STAT6 signaling pathway to promote the differentiation of tuft and goblet cells. Tuft cells further amplify this response by secreting IL-25, which enhances ILC2 activity in a positive feedback loop, aiding in innate immune responses against helminths (Gerbe et al., 2016; Sunaga et al., 2022).

M cells are specialized epithelial cells that transport luminal antigens to underlying lymphoid tissues, inducing mucosal immune responses. Their differentiation relies on receptor activator of nuclear factor κB ligand (RANKL) signaling from Peyer's patch stromal cells. Experimental mice lacking RANKL signaling failed to develop M cells. RANKL induce M cell differentiation in organoids (Knoop et al., 2009) and even outside of Peyer's patches (Kanaya et al., 2012). SPIB, a transcription factor downstream of RANKL signaling (van Es et al., 2019), is essential for M cell differentiation. Its deficiency in mice results in a complete absence of M cells, impaired T cell activation, and compromised musical immune response during Salmonella infection (Kanaya et al., 2012). Enteric neurons secreting calcitonin gene-related peptide (CGRP) modulate M cell differentiation by sensing pathogens and releasing CGRP. Loss of CGRP gene eliminates the dynamic control of M cell differentiation during Salmonella infection (Lai et al., 2020).

Enteroendocrine cells are very scarce, accounting for <1% of the total number of intestinal epithelial cells. These basal granule cells contain numerous secretory granules and exhibit neuronal-like traits, such as the ability to produce neurotransmitters and synapses-like structure (Beumer et al., 2020). The progenitors of enteroendocrine cells express neurogenin 3 (NEUROG3), which is inhibited by the Notch target HES1 (Beumer et al., 2020). NEUROG3 knockout eliminates all enteroendocrine cell subtypes in both the small and large intestine, while its overexpression increases their numbers (Li et al., 2021). The zinc finger transcription repressor GFI1 regulates secretory lineages fate, with its absence converting goblet and Paneth cells into enteroendocrine cells (Kolev and Kaestner, 2023). The differentiation of enteroendocrine cells is independent of the WNT signaling pathway, as β-catenin deletion in NEUROG3+ progenitors does not affect their development (Kolev and Kaestner, 2023; Kretzschmar and Clevers, 2017). Their differentiation requires reduced activity of the Notch and WNT pathways, a characteristic that distinguishes them from Paneth cells and absorptive cells.

Intestinal absorptive cells (enterocytes) are the most abundant cell type in the intestinal epithelium, responsible for absorbing ingested molecules. Notch signaling does not directly promote their differentiation but indirectly maintains their proportion by suppressing secretory lineage differentiation. When Notch signaling is inhibited in ATOH1-deficient crypts, absorptive cells develop normally and are even more abundant, likely due to reduction in secretory cell differentiation, which shifts progenitor cell fate toward the absorptive lineage (Kazanjian et al., 2010; Kim and Shivdasani, 2011). Their differentiation is further determined by the partial inhibition of WNT signaling, as demonstrated by the increased number of absorptive cells observed in organoid cultures under WNT pathway inhibition (Yin et al., 2014). Transcription factors hepatocyte nuclear factors HNF4A and HNF4G play a key role in the differentiation of absorptive cells, as knockout of HNF4G or both HNF4A and HNF4G significantly reduces absorptive cell numbers in organoids and mice (Lindeboom et al., 2018).

In the gut, SCFAs are produced through microbial fermentation of dietary fiber, mainly as acetate, propionate, butyrate, and small amounts of valerate, caproate, and isovalerate (Koh et al., 2016). SCFAs, especially butyrate, serve not only as an energy source for the host but also as regulators of the physiological functions of intestinal epithelial and immune cells (Marchix et al., 2018). They also play an important role in maintaining the integrity of the epithelial layer and tissue repair after intestinal mucosal damage. Butyrate may enhance epithelial barrier function by upregulating Claudin-1, activating HIF-1 pathway, or promoting tight junction protein assembly by activating AMPK signaling pathways (Suzuki, 2020; Kelly et al., 2015; Hodgkinson et al., 2023). It also regulates histone acetylation by activating low concentrations of histone acetyltransferase (HAT) or inhibiting high concentrations of histone deacetylase (HDAC) classes I and II (Hodgkinson et al., 2023; Abdalkareem Jasim et al., 2022). Research has demonstrated that the effects of butyrate on cell proliferation are dose-dependent and vary across different cell types. At concentrations below 2 mM, butyrate promoted colon cell proliferation, whereas higher doses in vitro suppressed the growth of human colon epithelial cells (Hodgkinson et al., 2023). Oral supplementation with butyrate enhanced the villus height to crypt depth ratio in juvenile animal models, such as piglets and calves (Wang et al., 2018). Intestinal epithelial cells, especially enteroendocrine cells, express G protein-coupled receptors (GPCRs), which are crucial for immune activation and signaling molecule metabolism. SCFAs activated at least three different G protein-coupled receptors: GPR41 (free fatty acid receptor 3; FFAR3), GPR43 (free fatty acid receptor 2; FFAR2) and GPR109A (hydroxy-carboxylic acid receptor 2; HCAR2) (Parada Venegas et al., 2019). For example, GPR41/43 activation dependent on SCFAs upregulates the production of colonic epithelial cytokines and chemokines, which helps to clear pathogens (Abdalkareem Jasim et al., 2022; Hodgkinson et al., 2023; Kimura et al., 2013). Among SCFAs, butyrate primarily activates the GPR109A receptor on intestinal epithelial cells or dendritic cells in the intestinal lamina propria, while acetate and propionate exert their effects by activating the GPR43/GPR41 receptors. Table 2 briefly summarizes the main characteristics of acetate, butyrate, and propionate.

Additionally, SCFAs enhance the production and release of mucus by goblet cells (Finnie et al., 1995). They specifically upregulate the expression of MUC genes in intestinal goblet cells (Fekete and Buret, 2023) and trigger Paneth cells in the small intestine to secrete α-defensin (Takakuwa et al., 2019), thereby strengthening the intestinal chemical barrier. Intestinal epithelial cells can also recognize certain byproducts such as SCFA or succinate produced by pathogens. For instance, intestinal tuft cells are chemosensors that can detect succinate produced by invading helminths. Upon activation, tuft cells trigger a type 2 innate immune pathway by producing IL-25 to clear the worms (von Moltke et al., 2016; Nadjsombati et al., 2018).

A small number of clinical trials and observational studies have found that butyrate plays a positive role in ulcerative colitis (UC) and inflammatory bowel disease (IBD). Through enema or oral administration of microencapsulated sodium butyrate, the clinical symptoms of UC or IBD patients can be improved, which may be closely related to its ability to enhance intestinal barrier function (Recharla et al., 2023; Facchin et al., 2020; Vernero et al., 2020; Scheppach et al., 1992). However, some studies have shown that butyrate enemas do not improve UC symptoms (Hamer et al., 2010). Further in-depth studies with larger sample sizes are needed.

Lactate is an organic acid produced by microbial fermentation of dietary fiber and other carbohydrates, such as lactose and glucose. Bifidobacteria, Lactobacilli, and Enterococci in the neonatal gut microbiota are the main producer of lactate, with some Staphylococci strains also capable of lactate production (Jost et al., 2012). Organoid models have confirmed that newly isolated Paneth cells from the mouse small intestine support intestinal stem cell function by providing lactic acid to enhance mitochondrial oxidative phosphorylation in Lgr5+ base columnar cells (Rodríguez-Colman et al., 2017). Recent studies have shown that lactate has unique biological activities, such as participating in the regulation of immune responses and tissue regeneration in the intestinal mucosa (Garrote et al., 2015). Lactate produced by microbial fermentation can reduce activation dependent on Toll like receptors (TLRs) and IL-1β pathways, thereby decreasing inflammatory responses in intestinal epithelial and bone marrow cells (Iraporda et al., 2015). In the Lgr5-GFP mouse model, oral administration of lactate-producing human probiotics (Bifidobacterium and Lactobacillus) significantly increased crypt height, as well as the number of Lgr5 intestinal stem cells, Paneth cells, and goblet cells in the small intestine (Lee et al., 2018). Further studies revealed that lactate signals through the G protein-coupled receptor GPR81 to induce intestinal stem cell proliferation. Additionally, pre-feeding with probiotics or lactate effectively protected mice from intestinal damage caused by radiotherapy and chemotherapy (Lee et al., 2018).

Clinical applications have also been explored, with probiotics containing Lactobacillus acidophilus and Bifidobacterium bifidum proving effective in alleviating diarrhea in cancer patients undergoing radiotherapy (Chitapanarux et al., 2010). These findings suggest that the use of lactobacilli symbionts or lactate salts may potentially prevent intestinal damage in humans during radiotherapy. Moreover, studies have shown that GPR81 expression is downregulated in the intestinal mucosal tissues of patients and mice with colitis. Oral administration of lactate has been found to enhance the expression of tight junction proteins, including Claudin-1, ZO-1, and Occludin, through GPR81, thereby alleviating experimental colitis and inhibiting the NF-κB/MMP9 signaling pathway (Li et al., 2024).

Bile acids are synthesized from cholesterol in the liver and are mostly reabsorbed by ileal epithelial cells after entering the intestine (de Aguiar Vallim et al., 2013). Approximately 90–95% of bile acids absorbed by epithelial cells are released into the ileal lamina propria through heterodimeric organic solute transport proteins OSTα and OSTβ on the epithelial cells (Li and Chiang, 2014). In addition to playing a key role in lipid digestion and absorption, bile acids also interact with intestinal epithelial cells to maintain intestinal homeostasis, regulate immune responses, and influence the gut microbiota. They regulate the functions of intestinal epithelial cells by activating nuclear receptors such as the farnesoid X receptor (FXR) and membrane receptors like the G protein-coupled bile acid receptor TGR5 (Fiorucci et al., 2010; Dhakal and Dey, 2022). These signaling pathways not only participate in the regulation of bile acid synthesis and metabolism but also affect intestinal barrier function, cell proliferation, and apoptosis. For example, the activation of FXR can enhance the integrity of the intestinal barrier and reduce intestinal inflammation (Verbeke et al., 2015; Gadaleta et al., 2011).

Bile acids play a dual role in maintaining intestinal barrier function (Hegyi et al., 2018). Primary bile acids, including cholic acid and chenodeoxycholic acid, may exert toxic effects on intestinal epithelial cells. In contrast, secondary bile acids, such as deoxycholic acid and lithocholic acid, can enhance intestinal barrier function by regulating the expression of tight junction proteins like Claudin and Occludin, although their effects may vary under different physiological or pathological conditions (Camilleri, 2022; Di Vincenzo et al., 2022). Moreover, bile acid metabolism disorders, such as excessive accumulation of secondary bile acids or impaired reabsorption of primary bile acids, are often associated with impaired intestinal barrier function. This may lead to increased intestinal permeability and contribute to the development of IBD (Long et al., 2023).

Research on bile acid signaling pathways has introduced new strategies for treating intestinal diseases (Wahlström et al., 2016). For example, FXR and TGR5 agonists have demonstrated preclinical benefits for IBD by regulating intestinal barrier function and suppressing inflammatory responses, making them promising candidates for treating IBD and metabolic disorders (Stepanov et al., 2013). Additionally, probiotics that regulate bile acid metabolism, such as by modulating gut microbiota composition or promoting the production of secondary bile acids, have also shown potential in managing diseases like IBD (Chen et al., 2019; Gadaleta et al., 2022).

Tryptophan and its metabolites play important roles in various physiological processes, including maintaining cell growth, being a component of proteins, and coordinating the organism's response to the environment as signaling molecules (Cervenka et al., 2017). There are several metabolic pathways for tryptophan in the gastrointestinal tract: (1) the kynurenine pathway, which accounts for approximate 95% of total tryptophan metabolism; (2) the indole pathway mediated by gut microbiota, which is the characteristic metabolic pathway in the intestine; (3) the 5-hydroxytryptamine (serotonin) pathway, accounting for about 1–2% tryptophan metabolism (Ghiboub et al., 2020; Zelante et al., 2013; Yu et al., 2024). While the kynurenine pathway dominates over tryptophan metabolism systemically, the indole pathway represents the major microbial-mediated metabolic route specifically within the gut environment.

Gut microbiota metabolize tryptophan into indole and its derivatives, such as indole-3-acetic acid and indolepropionic acid. These metabolites can activate the aryl hydrocarbon receptor (AHR), which is widely present in Paneth cells, goblet cells, intestinal stem cells, absorptive cells, and enteroendocrine cells. By activating AHR, these metabolites promote the proliferation of intestinal epithelial cells and expression of tight junction proteins, maintaining the integrity of the intestinal barrier, and regulating intestinal immunity. However, excessive activation of AHR may also contribute to inflammatory responses under certain pathological conditions (Roager and Licht, 2018). Metidji's research shows that AHR regulates Wnt/β-catenin signaling in intestinal epithelial cells, which helps to differentiate epithelial cells from crypt stem cells. Meanwhile, the absence of the aryl hydrocarbon receptor in intestinal epithelial cells leads to reduced expression of MUC2 and Car4, thereby weakening resistance to pathogenic bacterial infections (Metidji et al., 2019). Some members of the human gut microbiota, such as Clostridium sporogenes, have been found to decarboxylate tryptophan, leading to the production of the neurotransmitter tryptamine (Williams et al., 2014). Furthermore, Clostridium sporogenes can lead to the production of indole acetic acid and indole propionic acid, both of which affect intestinal permeability and host immunity (Dodd et al., 2017; Lamas et al., 2018). Tryptophan and indole active transport proteins have been identified in Escherichia coli. These studies indicate that indole, a tryptophan metabolic product dependent on the microbiota, plays an important role in maintaining the integrity of the epithelial barrier.

Intestinal epithelial cells express various innate receptors, including TLRs, NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), and C-type lectin receptors (CLRs). These receptors rapidly recognize microorganisms and their components (such as lipopolysaccharides, peptidoglycan, flagellin,), activate downstream signaling pathways, and subsequently promote epithelial cell proliferation as well as the expression and secretion of various cytokines and chemokines. However, excessive activation of these receptors may also lead to pathological inflammation or epithelial damage under certain conditions. This complex receptor network is essential for maintaining intestinal health and defending against pathogen invasion.

In the small intestine, Paneth cells secrete the antimicrobial peptides RegIII-β, RegIII-γ, and α-defensins in a TLR/MyD88-dependent manner under homeostatic conditions. These antimicrobial peptides play critical roles in inhibiting the proliferation of pathogenic bacteria and maintaining the balance of the intestinal microbiota (Gong et al., 2010). In the colon, goblet cells require TLR/MyD88 signaling to achieve compound mucin granule exocytosis. TLR ligands, including lipopolysaccharides and flagellin, can induce colonic goblet cells to secrete MUC2 (Birchenough et al., 2016). Studies have shown that MyD88 deficiency in intestinal epithelial cells leads to reduced expression of MUC2 and decreased production of antimicrobial peptides, particularly RegIII-γ, showing a high sensitivity to colitis and Salmonella enterica serovar Typhi or Citrobacter infection (Frantz et al., 2012; Vaishnava et al., 2011).

NLRs are innate cytoplasmic receptors that also participate in maintaining mucosal barrier function. Studies have shown that the activation of NLRP6 in the NLR family promotes the secretion of mucin granules by goblet cells, which is crucial for preventing the proliferation of colitis bacteria (such as Prevotellaceae) (Wlodarska et al., 2014). Intestinal endocrine cells, Paneth cells, and goblet cells can specifically express Chitinase 3-like protein 1 (Chi3l1) and secrete it into the intestinal lumen when stimulated by the gut microbiota. Chi3l1 interacts with the gut microbiota through the cell wall component peptidoglycan, affecting the colonization of Gram-positive bacteria. This interaction not only prevents colitis but also contributes to the regulation of immune responses and the maintenance of the intestinal barrier (Chen et al., 2024).

Some commensal bacteria have evolved specific strategies that allow them to adhere to the intestinal mucosal surface and induce the expression of specific genes in intestinal epithelial cells, which is related to the intrinsic features of the bacteria.

Segmented filamentous bacteria (SFB) are natural gut commensals. Through comparative studies in humans, mice, and chickens, it has been found that while SFB distribution in the gastrointestinal tract shows species specificity, the small intestine (particularly the ileum) serves as the primary colonization site across all studied species (Yin et al., 2013). SFB communicates with host ileal epithelial cells through endocytic vesicles formed at the SFB-epithelial cell synaptic interface. These vesicles contain SFB cell wall-associated proteins P3340 that can induce the activation of antigen-specific Th17 cells in the lamina propria by promoting antigen presentation. This confirms direct communication between resident gut microbiota and the host, and indicates that under physiological conditions, intestinal epithelial cells acquire antigens from commensal bacteria to generate T cell responses to the resident microbiota (Ladinsky et al., 2019; Yang et al., 2014). SFB colonization in the small intestine promotes overall transcriptional changes in host epithelial cells, including the induction of antimicrobial peptides and stress response genes, such as serum amyloid A (SAA1 and SAA2) (Ivanov et al., 2009).

Unlike SFB, which colonizes the small intestine, Bacteroides predominantly resides in the colonic crypts. Bacteroides plays a crucial role in maintaining gut microbiota balance by fermenting polysaccharides to produce short-chain fatty acids. Studies (Lee et al., 2013) in germ-free mice showed that animals were easily colonized first by Bacteroides fragilis, followed by Bacteroides thetaiotaomicron or Bacteroides vulgatus, with the sequence of microbial exposure having no effect on colonization results. Further investigation showed that intestinal Bacteroides possess conserved polysaccharide utilization loci, known as commensal colonization factors (CCF). During intestinal colonization, the CCF gene in Bacteroides fragilis are upregulated. Deletion of the CCF gene in the symbiont Bacteroides fragilis led to colonization defects and reduced horizontal transmission in mice. Notably, mutant strains lacking CCF failed to penetrate deep into the colonic crypts despite binding to the epithelial surface. These findings demonstrate that intestinal Bacteroides have developed unique, host-specific interactions that ensure stable and resilient gut colonization, with the CCF serving as an innovative mechanism driving this symbiotic relationship (Lee et al., 2013).

The intrinsic features of commensal bacteria play a crucial role in their ability to interact with intestinal epithelial cells and establish stable colonization. Understanding these interactions provides valuable insights into the dynamic relationship between gut microbes and their host, offering potential avenues for advancing gut health research.