The major intestinal SCFAs, including acetate, propionate and butyrate, are primarily produced by gut microbiota via fermentation of indigestible carbohydrates. Acetate is generated by Bacteroidetes, Bifidobacterium and Clostridium through the acetyl-CoA or Wood-Ljungdahl pathways. Propionate is synthesized by Bacteroidetes and Clostridium spp. via succinate, acrylate, or propylene glycol pathways. Butyrate is mainly derived from Firmicutes through acetyl-CoA condensation or acetate coenzyme A-transferase pathways (facilitated by gut fungi, such as Morchella) (18,46–51).

SCFAs serve as energy sources for intestinal cells and signaling molecules in systemic circulation and modulate tissues, such as the liver and adipose tissues (52). They exert anti-inflammatory effects by regulating cytokines and immune cell activity. The maternal gut and blood have elevated levels of SCFAs during pregnancy, which cross the placenta to influence fetal immunity (53). Notably, acetic acid administration induces abortion in 24 h (54) and a higher propionate/acetate ratio in early pregnancy is associated with increased inflammation and relapse in women with multiple sclerosis (55). This highlights the critical role of SCFAs in maintaining healthy pregnancies.

As shown in Fig. 1, SCFAs promote CD8⁺ memory T cell formation and regulate Th1, Th17 and Treg differentiation to maintain intestinal homeostasis. They enhance tolerogenic DCs in the gut, inducing Treg differentiation (56) and modulating immune cells via humoral/glycolipid pathways. Pathogen-induced Th17 cells rely on anaerobic glycolysis and oxidative phosphorylation (OXPHOS), while commensal microbiota-induced Th17 cells depend only on OXPHOS (52). SCFAs act through G protein-coupled receptors (GPR43/FFAR2, GPR41/FFAR3, GPR109A/HCAR2) to trigger signaling cascades such as ERK and STAT3. This leads to upregulation of IL-10 and Foxp3 gene expression, promoting Treg differentiation (57–59). They also inhibit HDACs (such as class I), increasing histone acetylation at Foxp3 loci to stabilize Tregs and suppress pro-inflammatory genes in other T-cell subsets (60,61). The reduction in SCFAs caused by the dysbiosis of gut microbiota can weaken these mechanisms, leading to Th17/Treg imbalance and inflammation at the maternal-fetal interface that contribute to RPL (62). SCFAs may prevent pregnancy complications by enhancing anti-inflammatory cytokines (such as IL-10) and Treg differentiation (63).

BAs are synthesized from cholesterol in the liver mostly via the classical pathway, producing cholic and chenodeoxycholic acids. They are secreted into the intestine, where they play a role in lipid digestion and regulate metabolism, signaling pathways and composition of gut microbiota (64,65). Gut microbiota metabolize primary BAs into secondary BAs via deconjugation, hydroxylation, dehydration, or epimerization, involving species, such as Bacteroides and Bifidobacterium (66,67). BAs activate thyroid hormone-activating enzyme D2, influencing energy expenditure. Their serum levels fluctuate with thyroid function, which is critical for fetal brain development (68).

Elevated maternal serum BA levels during pregnancy increase risks of adverse outcomes such as stillbirth (69). BAs regulate immune function by modulating the expression of immune genes and cell activity. They bind to rarnesoid X receptor (FXR) and G protein-coupled receptor for bile acids 1 (GPBAR1) to inhibit NF-κB activation, thereby suppressing pro-inflammatory cytokine transcription; they also modulate NOD-like receptor thermal protein domain associated protein 3 inflammasome activity and Th17/Treg balance (70). Conversely, BA-induced GPBAR1 activation triggers NF-κB in trophoblasts, promoting placental inflammation and abnormal leukocyte infiltration (Fig. 2), which could return to affect pregnancy (24). Murine models showed placental inflammation at serum BAs >40 µmol/l, while human intrahepatic cholestasis of pregnancy (ICP) exhibited variable thresholds (10–100 µmol/l), indicating species-specific vulnerability (71,72).

BAs also regulate bile acid homeostasis via enterocyte L-cell receptors, activating FXR-Retinoid X Receptor (RXR) dimerization to induce ileal bile acid-binding protein, Oxysterols and hormones, which inhibit apical sodium-dependent bile acid transporter (73,74). This modulates entero-hepatic innate immunity, maintaining tolerogenic phenotypes (52). BAs were traditionally thought to promote inflammation due to their accumulation in the livers of patients with liver diseases and disrupt cellular membranes. However, they have anti-inflammatory properties, particularly in the innate immune system. Two life cycle assessment metabolites, 3-oxoLCA and isoalloLCA, can directly affect CD4+ T cells, suppressing Th17 differentiation and enhancing Treg differentiation (75,76).

Indoles, microbial metabolites of tryptophan (Trp), are produced by >85 bacterial species (such as Fusobacterium, Escherichia coli and Bacteroides) via tryptophanase-mediated conversion) (77). Clostridium further metabolizes Trp into derivatives such as tryptamine, indole-3-lactate and indole-3-acetate (I3A); deficiencies in tryptamine and I3A accelerate inflammation. Indole-3-propionate and other derivatives, such as indole-3-aldehyde, act via AHR to modulate immune responses (78).

As shown in Fig. 3, plasma Trp levels decrease during pregnancy, which might be linked to immune activation (79). Indoles activate AHR, critical for gut epithelial barrier maintenance, and regulate T-cell subsets (Th17, FOXP3⁺ Tregs and Tr1) (43). AHR activation by indoles balances immunity by promoting Tr1 conversion and influencing early Th17 differentiation; Th17 cells are associated with adverse pregnancy outcomes. Additionally, microbial Trp metabolites regulate placental vascular development via AHR (78). However, indole-based compounds (such as I3C) may induce fetal mortality. Moreover, I3A exposure during rat gestation days 12–14 could cause microencephaly, highlighting context-dependent effects.

Indoleamine 2,3-dioxygenase (IDO), expressed in placental syncytiotrophoblasts and blastocyst membranes, catalyzes Trp degradation and may contribute to pregnancy immunosuppression. High-fat diets upregulate IDO, shifting Trp metabolism from indole to kynurenine production, thereby reducing insulin sensitivity. Lactobacillus reuteri produces an indole derivative of Trp, which activates AHR in CD4+ T cells and downregulates T-helper-inducing POZ/Krüppel-like factor (ThpoK), enabling the differentiation of CD4+ T cells into double positive intraepithelial lymphocytes with immunomodulatory function. Mammalian fetuses can survive an immune attack of the maternal T cells by preventing the release of L-Trp via IDO (80,81). IDO may induce potent anti-inflammatory and antioxidant effects in pregnant women. This highlights the crosstalk between gut microbiota and immune cells in reproductive organs.

In summary, pregnant women exhibit increased inflammatory processes in the placenta, characterized by hypoxia, elevated vascular density and reduced placental maturity. Meanwhile, alterations in dietary habits, sleep patterns and hormonal profiles during pregnancy might affect the composition of gut microbiota (75). SCFAs production is associated with genes, such as free fatty acid receptors 1–4, and plays a role in regulating immune cells (such as Tregs, Th17 cells and effector T cells) (82,83). They affect pregnancy outcomes by altering the composition of gut microbiota and fetal metabolic programming. BAs, encoded by genes, including IBABP and FXR, aid in fat digestion in the intestine. They also regulate immune cells, such as T cells, B cells and DCs (84). In pregnancy, elevated levels of BAs can induce inflammation, cause respiratory distress in newborns and lead to meconium-stained amniotic fluid. Indoles, as tryptophan metabolites, encompass various derivatives. Encoded by genes such as NRF2 and AHR, they regulate immune cells expressing cytokines, such as IL-6 and TNF-α and are critical for key pregnancy processes, including placentation. Specifically, indoles can activate the pregnane X receptor (PXR) to exert anti-inflammatory effects. Furthermore, excessive production of certain microbial by-products, such as fatty acids, BAs, indoles and their derivatives, is a hallmark of leaky gut syndrome. Gut-derived lipopolysaccharides drive macrophages toward the pro-inflammatory M1 phenotype, impairing trophoblast invasion. This is followed by the activation of inflammatory response-related cytokines, such as Th17 cells, Tregs, NK T cells, CD4+/CD8+ T cells and various ILs. Consequently, these cascading events may exert detrimental effects on fetal development and nutrient supply. The underlying mechanism of crosstalk between gut microbiota and immune cells in RPL (48,67,85) is summarized in Table II and Fig. 4.

Emerging clinical evidence supports the use of specific probiotic strains to correct dysbiosis of gut microbiota and immune imbalances in RPL (86). Lactobacillus-dominated interventions, such as the vaginal or oral administration of L. crispatus and L. rhamnosus, have been shown to increase the endometrial abundance of Lactobacillus (>90%), which was associated with improved implantation rates (OR=3.7; P<0.01) and reduced miscarriage risk in randomized controlled trials patients. This is attributed to enhanced IL-10 production, Treg induction and the suppression of pathogenic biofilm formation by Gardnerella and Streptococcus. The bacterial strains, such as Clostridium butyricum and Faecalibacterium prausnitzi (administered orally), markedly elevate fecal butyrate levels (>40–60%) and increase peripheral blood Treg frequencies (>2.1-fold) in RPL patients, concomitant with reduced Th17-mediated inflammation. A recent randomized controlled trial (n=850) reported a non-significant increase in clinical pregnancy rates and a slight reduction in miscarriage risk with probiotics treatment (87). Taken together, these findings underscore that the probiotic interventions, whether Lactobacillus-dominated or SCFA-producing, act through complementary pathways to correct the microbial and immune dysregulation underlying RPL. By restoring Lactobacillus dominance in the endometrium or enhancing SCFA-mediated immune modulation, these strains offer targeted, microbiota-based strategies to improve reproductive outcomes in women with RPL.

Some studies suggest that FMT may offer a potential therapeutic approach for RPL by restoring a healthy gut microbiota, which plays a crucial role in immune regulation and pregnancy maintenance. FMT from healthy donors has demonstrated efficacy in reducing pregnancy loss. FMT from normal pregnant women to abortion-prone dams restored gut microbial diversity, the Chao1 index was negatively associated with the changes in IL-17A and IFN-γ and the Shannon index was negatively associated with changes in IL-17A levels (88). Pilot human studies are underway (NCT04817969), evaluating FMT for unexplained RPL (11,89), with preliminary data showing normalization of BA and SCFA profiles in 70% of recipients. Together, these findings bridge preclinical promise with early clinical progress, suggesting that FMT might one day address a significant unmet need in RPL treatment, particularly for cases where traditional approaches have failed (90,91). With the advances in research, further exploration of the precise mechanisms linking gut microbial balance to pregnancy success, along with large-scale clinical trials, will be crucial to validating the efficacy and safety of FMT in reproductive care.

Increased dietary fiber intake (≥30 g/day) during pregnancy, a key modulator of reproductive health, has been linked to improved pregnancy outcomes. The consumption of such fiber can elevate fecal SCFA levels, specifically butyrate, by 3–4-fold. Cohort studies have further associated high fiber intake with a lower risk of miscarriage (92). This beneficial effect is rooted in fiber's role as a critical substrate for beneficial gut bacteria, including Bifidobacterium and Roseburia, which metabolize it to produce immune-modulating metabolites that help maintain a pregnancy-supporting environment. In addition to general dietary fiber intake, targeted dietary patterns rich in complementary nutrients have also shown promise. For instance, Mediterranean diet interventions, characterized by high levels of polyphenols and fiber, have been found to markedly reduce inflammatory cytokines, with >40% reductions in IL-6 and >30% reductions in TNF-α in women with RPL who are attempting new pregnancies. Concurrently, these interventions improve the function of Tregs, which play a pivotal role in suppressing harmful immune responses against the fetus (93,94). Notably, the metabolic byproducts of fiber fermentation, such as butyrate, have been directly investigated for their therapeutic potential. Butyrate supplementation effectively reverses dysbiosis in female mice, markedly increases Treg cell populations and decreases preterm birth rates, highlighting the metabolite's direct role in supporting implantation and fetal retention (95). Similarly, interventions targeting other inflammatory pathways in high-risk pregnancies have yielded positive results. For women with ICP, cholestyramine therapy has proven effective. A review demonstrated that in women with unexplained recurrent spontaneous abortion (URSA), the butyrate supplementation could reduced uterine NK cell cytotoxicity and impact Treg cell level (95). It also normalized TNF-α/IL-10 ratio, which has been linked to endometriosis and pregnancy failure (37,96). Notably, butyrate-producing bacteria play an important role in pregnancy maintenance. It reduces the risk of preterm birth (OR=0.3) and stillbirth (OR=0.2) by lowering serum BA levels and inhibiting placental inflammation, thereby addressing a condition where BA accumulation triggers harmful inflammatory cascades. Additionally, bioactive compounds derived from dietary sources have shown promise in preclinical models. I3C, a compound found in cruciferous vegetables, activates AHR signaling in murine RPL models. This activation suppresses aberrant Th17 cell responses, which drive inflammation and fetal loss and ultimately prevents pregnancy failure (43). Collectively, these findings highlight a consistent theme: Dietary components, their microbial metabolites and targeted supplements can exert profound effects on pregnancy outcomes by modulating immune function, reducing inflammation and restoring balance to the pathways critical for fetal survival. From fiber's role in nurturing beneficial gut bacteria to specific metabolites and compounds that directly regulate immune cell activity, these interventions offer promising avenues for improving reproductive health in at-risk populations.