FMT restores intestinal microecological balance by introducing donor microbiota into the recipient’s gut, thereby significantly improving the intestinal microbial environment. This includes enhancing α-diversity (richness and evenness of microbial communities) as well as β-diversity (differences in microbial composition among populations). Specifically speaking, FMT expands α-diversity of the receiver’s gut, and the microbiota profile of the receiver becomes more similar to healthy donor microbiotas. Increased α-diversity is positively correlated with increased bowel movement frequencies among FC patients. Furthermore, the restoration of α-diversity is often accompanied by an increase in key metabolic products, such as short-chain fatty acids (SCFAs), which are instrumental in sustaining intestinal barrier homeostasis and improving bowel function (8, 9). And β-diversity FMT expands similarity among donor and receiver microbiotas. It’s manifested not only at the general level of the structure of the community, but at transplantation and steady establishment of key microbial species, respectively (10, 11). After FMT, for example, there’s reappearance of Faecalibacterium prausnitzii in the receiver’s gut, and it’s closely connected with clinical symptom amelioration (7). Donor source of FMT and treatment times exert significant influences on the scale of restoration. Healthy donor sources tend toward more lasting restoration of improvements, and repeat transplantation achieves superior steady reconstruction of microbiotas toward a single transplantation (7, 12).

In patients with FC, the gut microbiota imbalance is not only reflected in the overall reduction of diversity but also in specific structural changes. Studies have shown that common characteristics of this imbalance include an increased Firmicutes/Bacteroidetes ratio, reflecting increased Firmicutes abundance, decreased Bacteroidetes, along with an increase in certain opportunistic pathogens, while beneficial bacteria are reduced (13, 14). At the family and genus levels, microbiota associated with short-chain fatty acid (SCFA) production, such as Muribaculaceae and Bacteroides, tend to decrease, while certain opportunistic pathogens, including Enterobacteriaceae and Clostridium sensu stricto, tend to increase. These changes are closely related to gastrointestinal motility disorders (15, 16).

Following FMT intervention, these structural imbalances gradually recover. At the phylum level, the ratio of Firmicutes to Bacteroidetes tends to normalize, reflecting the reconstruction of intestinal homeostasis. Notably, at the family level, increases in the abundance of key taxa such as Prevotellaceae and Ruminococcaceae, contribute to enhanced the production of short-chain fatty acids (SCFAs) and secondary bile acids. At the genus level, there is a marked restoration of Faecalibacterium and Roseburia, both of which are butyrate-producing bacteria. Butyrate serves as the main energy substrate for colonic epithelial cells, promotes intestinal motility, and enhances barrier function (17). Meanwhile, the proportion of opportunistic pathogens decreases (16, 18). These changes suggest that FMT reshapes the microbiota composition, restores metabolic function, and establishes a foundation for balancing the downstream bile acid profile and activating receptor signaling. Table 1 summarizes the major effects of FMT on gut microbiota in patients with FC (Table 1).

In addition to functional constipation, evidence from other clinical contexts suggests that fecal microbiota transplantation can induce comparable shifts in gut microbial composition. In the study by DuPont et al., which examined microbiota changes following FMT in PD patients, the genera Roseburia and Ruthenibacterium became among the 10 most prevalent taxa during and after treatment, although they were not among the dominant genera at baseline. Roseburia belongs to the butyrate-producing Lachnospiraceae family (Firmicutes phylum), while Ruthenibacterium spp. are members of the Ruminococcaceae family, well known for producing short-chain fatty acids and contributing to gut barrier integrity and immune function. Ruthenibacterium spp. have previously been detected in the intestinal microbiota of PD patients. In addition, Collinsella emerged as one of the most common genera following FMT. Collinsella (Actinomycetota/Actinobacteria) has been associated with protection against SARS-CoV-2 infection and was shown to decrease during weight-loss interventions in obese patients with type 2 diabetes. Other Firmicutes taxa, including Limnochordaceae, Peptostreptococcaceae, and Lactobacillaceae, also increased significantly after FMT. However, there is currently no evidence indicating that increased abundance of members of the Limnochordaceae family confers specific health benefits (19).

Bile acid metabolism relies on the critical process of the enterohepatic circulation, in which most bile acids are reabsorbed in the terminal ileum via the portal circulation and transported back to the liver (20). Only a small proportion of primary bile acids, such as Cholic Acid (CA) and Chenodeoxycholic Acid (CDCA), escape absorption in the small intestine and enter the colon. There, through enzymatic reactions such as 7α-dehydroxylation mediated by bacterial genera including Clostridium scindens, they are converted into secondary bile acids, including Deoxycholic Acid (DCA) and Lithocholic Acid (LCA) (21, 22). In healthy individuals, secondary bile acids typically dominate the fecal bile acid profile. This is dependent on the cooperative actions of various microbiota species, such as those carrying bile salt hydrolase (BSH), which catalyze the deconjugation reaction and provide substrates for subsequent 7α-dehydroxylation (23, 24).

Research evidence indicates that patients with constipation often exhibit an increased proportion of primary bile acids and a marked reduction in secondary bile acids, suggesting a functional impairment in the bile acid conversion process (25). This imbalance not only indicates the loss of key functional microbiota but may also lead to insufficient activation of downstream receptors such as FXR and TGR5, then affecting intestinal motility and secretory function. FMT can partially restore this imbalance. Experimental studies have shown that FMT elevates secondary bile acid concentrations while reducing primary bile acid proportions in recipient feces, resulting in a bile acid profile that gradually approximates that of healthy donors (26–28). This suggests that FMT not only alters the microbiota composition but also restores the balance between primary and secondary bile acids by rebuilding microbial functional groups, thereby providing a foundation for the activation of FXR/TGR5 signaling and improvement in clinical symptoms.

In addition to primary and secondary bile acids, FMT may also influence other derivatives, such as ursodeoxycholic acid (UDCA). These metabolites play a potential role in maintaining gut barrier integrity and microbiota homeostasis. However, direct evidence linking these metabolites to constipation remains limited (29). Table 2 summarizes the main primary and secondary bile acids, the microbial processes involved, and their major receptor pathways (Table 2).

The reestablishment of the ratio between primary and secondary bile acids restores secondary bile acids as effective agonists of TGR5, while maintaining the sustained stimulation of FXR by primary bile acids (30, 31). This indicates that the restoration of the bile acid profile is not only a metabolic outcome but also represents the reestablishment of receptor signaling pathways. Therefore, the therapeutic effect of FMT on FC can be understood as a progressive process: initially, bile acid metabolism is reestablished through microbial modulation, primary and secondary bile acids act as signaling mediators to activate FXR and TGR5 pathways. The following section will elaborate on the specific manifestations of this receptor activation pattern.

After FMT, gut microbiota remodeling significantly increases the concentration of CDCA in the ileum (32). CDCA, as an endogenous ligand for FXR, can directly activate FXR (33). Once activated, FXR plays a pivotal role in maintaining bile acid homeostasis by inhibiting the activity of cholesterol 7α-hydroxylase (CYP7A1), while simultaneously facilitating the generation of primary bile acids, including CA and CDCA (34). Furthermore, FXR activation in intestinal epithelial cells stimulates fibroblast growth factor 19 (FGF19) secretion, thereby establishing a “gut–liver axis” feedback loop. This axis further fine-tunes hepatic bile acid synthesis and integrates bile acid signaling with energy metabolism (35).

Representative secondary bile acids, including DCA and LCA, exhibit high binding affinity for TGR5 and activate this receptor when they accumulate in the colon (36). Activation of TGR5 stimulates the synthesis of cyclic Adenosine Monophosphate (cAMP) through the Gs protein–coupled signaling pathway, which subsequently leading to activation of downstream Protein Kinase A (PKA) (37), ultimately inducing the expression and release of 5-Hydroxytryptamine (5-HT) (38).

5-HT, as a key neurotransmitter in the gut, not only promotes chloride and water secretion, softening stool (39), but also enhances smooth muscle contraction and colonic propulsive motility by stimulating the enteric nervous system. In addition, TGR5 activation stimulates enteroendocrine L cells to release Glucagon-like peptide-1 (GLP-1), which, similar to 5-HT, works in concert to promote motility and secretion (40). Clinical studies have further confirmed that, following FMT treatment, patients with constipation exhibit a significant increase in 5-HT levels within the colonic mucosa, along with enhanced 5-HT expression on intestinal epithelial cell surfaces, thereby effectively enhancing intestinal secretion and propulsive motility (41). Results from animal experiments demonstrate that in TGR5 knockout mice, the colonic propulsion rate increased by only 18% after FMT intervention, which was markedly lower than the 42% observed in wild-type mice (p < 0.05). This provides compelling evidence that TGR5 plays an indispensable role in the pro-motility effects induced by FMT (42, 43).

FXR and TGR5, both bile acid–dependent receptors, cooperate to maintain bile acid homeostasis and intestinal function. FXR activation can upregulate the expression of TGR5, and the coordinated activity of these receptors promotes the GLP-1 secretion from L cells, thereby further enhancing intestinal propulsive function (44). Additionally, the use of an FXR-selective agonist alone has limited effects on metabolic improvement, but when combined with TGR5 activation, it can more effectively correct bile acid imbalance and microbiota abnormalities (45).

Although the involvement of FXR and TGR5 receptors has been confirmed in multiple studies, there are still discrepancies between studies. In animal experiments, both FXR and TGR5 are often activated after FMT (6). However, in clinical patients, the improvement in constipation symptoms following FMT is more strongly associated with the activation of the FXR pathway. This difference may be related to factors such as the donor microbiota composition, the patients’ bile acid levels, and the method of microbiota transplantation (46–48).

Additionally, the dysbiosis patterns of the microbiota differ across constipation subtypes, leading to variations in bile acid metabolites. In slow-transit constipation (STC), the deficiency of secondary bile acids results in impaired TGR5 signaling. FMT can restore its function by rebuilding microbiota that produce secondary bile acids (49, 50). On the other hand, outlet obstruction constipation (OOC) is often accompanied by localized inflammation and barrier damage, making it more reliant on compensatory FXR activation to maintain mucosal barrier integrity and bile acid homeostasis (51).