The gut fungal community's role in brain development disorders: how multiple gut microbes may affect the gut-brain connection

Intestinal epithelial barrier integrity remains debated in ASD pathophysiology. While the “leaky gut” hypothesis—uncontrolled translocation of microbial products into circulation—is frequently cited, clinical evidence is heterogeneous. Early studies reported abnormal intestinal permeability in ∼37% of children with ASD versus <5% of controls, rising above 40% in those with gastrointestinal symptoms (de Magistris et al., 2010; Fattorusso et al., 2019).

However, subsequent well-controlled investigations have challenged the universality of this dysfunction. For instance, Dalton et al. (2014) utilized the lactulose/mannitol (L/M) recovery ratio—a gold standard for permeability assessments—and found no significant differences between children with ASD and age-matched controls with special educational needs (mean L/M ratios: 0.015 vs. 0.014, respectively). Similarly, Kushak et al. (2016) reported no statistically significant difference in permeability between children with ASD and non-autistic children when controlling for gastrointestinal symptoms, suggesting that barrier dysfunction may be more closely associated with general gastrointestinal distress rather than ASD per se. Notably, Alookaran et al. (2022) found no significant elevation in fecal calprotectin or serum Dectin-1 levels in children with ASD compared to controls, further challenging the notion that fungal dysbiosis is invariably linked to gut inflammation in ASD. These discrepancies indicate that increased intestinal permeability is likely not a ubiquitous feature of ASD but rather a pathological trait specific to a subset of individuals, particularly those with severe ASD phenotypes or specific inflammatory profiles, rather than being exclusively associated with gastrointestinal comorbidities.

In the subset of individuals where barrier integrity is compromised, fungal dysbiosis is posited to act not merely as a passive observer but as an potential active modulator of epithelial function. C. albicans, the most prevalent fungal pathobiont, possesses distinct mechanistic capabilities to exploit and exacerbate barrier vulnerability. (1) Direct mechanical and cytotoxic disruption: through morphological plasticity, C. albicans transitions from a commensal yeast to an invasive hyphal form. This transition, as demonstrated by Dalle et al. (2010), facilitates physical adhesion to the epithelium and penetration of epithelial cell layers via both induced endocytosis and active penetration, ultimately leading to compromised epithelial barrier function. Concurrently, fungal metabolic activity produces cytotoxic compounds, such as ammonia, which can damage the mucosal lining and further weaken epithelial coherence (Ene et al., 2014). (2) Immunological modulation of tight junctions: the morphological plasticity of C. albicans enables its transition from a commensal yeast to an invasive hyphal form. This transition is associated with increased adhesion to epithelial surfaces and tissue penetration. Crucially, the hyphal form exposes specific PAMPs, which are recognized by host pattern recognition receptors (PRRs) on epithelial and immune cells. This recognition triggers potent proinflammatory signaling cascades (e.g., via NF-κB), leading to the production of cytokines such as IL-1β and TNF-α. These inflammatory mediators are known to downregulate the expression and alter the organization of tight junction proteins, thereby compromising epithelial barrier integrity. Thus, the hyphal transition contributes to barrier dysfunction primarily by initiating a host inflammatory response that disrupts tight junction complexes, rather than through direct physical disruption alone.

Consequently, while fungal dysbiosis may not be the primary initiator of barrier dysfunction in all patients with ASD, it likely functions as a critical modifier in vulnerable individuals. A bidirectional feedback loop may emerge in this specific subgroup: an initial genetic or environmentally induced barrier defect creates a niche permissive for fungal overgrowth; established fungal populations then employ direct invasion and inflammatory signaling to further degrade the barrier. This cycle facilitates the translocation of microbial metabolites and neuroactive compounds, potentially linking localized gut dysfunction to the systemic immune activation and neurobehavioral exacerbations observed in patients with the ASD phenotype.

Beyond the gut mucosa, fungal dysbiosis in ASD is implicated in systemic immune dysregulation. The immune response to fungal overgrowth, particularly Candida species, creates a chronic inflammatory milieu paralleling immune profiles observed in ASD subsets mediated by fungal antigen-host immune interactions driving proinflammatory signaling (Hughes and Ashwood, 2018).

The primary mechanism linking fungal dysbiosis to systemic inflammation involves the recognition of fungal cell wall components, particularly β-glucans, by PRRs on host immune cells. Dectin-1, a C-type lectin receptor expressed on dendritic cells and macrophages, binds β-glucans and activates the spleen tyrosine kinase–caspase recruitment domain-containing protein 9 (Syk–CARD9) signaling axis (Brown, 2006; Iliev et al., 2012). This pathway leads to assembly of the Bcl10–MALT1 complex, ultimately activating NF-κB to induce expression of proinflammatory cytokines including IL-6, IL-23, IL-1β, and TNF-α (Iliev et al., 2012; Li et al., 2019). This signaling cascade acts synergistically with TLR stimulation to activate the NACHT, LRR and PYD domains-containing protein 3 (NLRP3), which processes pro-cytokines into their mature, active forms (Brown, 2006; Gringhuis et al., 2012; Iliev et al., 2012; Li et al., 2019). The critical role of CARD9 in antifungal immunity is underscored by human CARD9 deficiency—the only known inborn error of immunity that predisposes to both mucosal and invasive candidiasis with unique CNS tropism (Lionakis et al., 2023).

Notably, the immune response to fungal pathogens is intrinsically linked to the Th17 pathway. Candida antigens stimulate the differentiation of naïve T cells into Th17 cells, which produce interleukin-17 (IL-17) and IL-22 (Acosta-Rodriguez et al., 2007). While IL-17 is essential for acute mucosal defences against fungal infections, its chronic elevation is pathogenic (Wu et al., 2021). Sustained high levels of IL-17 suppress the function of regulatory T cells (Tregs), thereby eroding immune tolerance and promoting continuous tissue damage and autoimmunity (Wang Q. et al., 2025; Zheng et al., 2020). Elevated IL-17 levels are a reproducible finding in patients with ASD (Gładysz et al., 2018) and have been mechanistically linked to neurodevelopmental deficits in maternal immune activation (MIA) models (Choi et al., 2016; Gładysz et al., 2018). The evidence from animal models suggests a potential link between interleukin-17A (IL-17A) and neurodevelopment: in MIA studies, circulating IL-17A may cross the placental barrier during gestation and possibly the BBB, binding to interleukin-17 receptor A (IL-17RA) expressed on neural cells, including neurons and microglia (Choi et al., 2016; Gładysz et al., 2018). This binding is associated with microglial activation and neuroinflammatory responses, which could contribute to synaptic dysfunction (Choi et al., 2016; Gładysz et al., 2018). In experimental settings, these processes have been linked to cortical disorganization and altered neural connectivity, correlating with behavioral abnormalities like social deficits and repetitive behaviors observed in individuals with ASD (Choi et al., 2016; Gładysz et al., 2018). Immune dysregulation, as highlighted in clinical studies, may perpetuate IL-17-mediated neuroinflammation, although direct human evidence for barrier penetration remains limited (Choi et al., 2016; Gładysz et al., 2018). Consequently, fungal dysbiosis may serve as a continuous endogenous source of IL-17, potentially contributing to a neuroinflammatory state, though direct causal evidence in human subjects is currently limited.

Furthermore, the assertion that intestinal fungal dysbiosis leads to systemic immune activation is supported by serological evidence. A study by Hughes and Ashwood (2018) identified significantly elevated levels of anti-C. albicans IgG antibodies in the plasma of children with ASD compared to neurotypical controls (36.5% vs. 14.3% positivity). The presence of IgG antibodies indicates a systemic adaptive immune response to fungal antigens, suggesting that these antigens have likely breached the intestinal barrier to interact with circulating immune cells (Hughes and Ashwood, 2018). Importantly, this antibody response was not strictly correlated with current gastrointestinal symptoms, implying that fungal-driven immune activation can occur even in the absence of overt gastrointestinal distress, acting as a “silent” driver of systemic dysregulation (Hughes and Ashwood, 2018).

Additionally, the chronic antigenic load from fungal dysbiosis further disrupts the homeostatic balance between proinflammatory cells and Tregs. The persistent drive toward Th1 and Th17 differentiation in response to fungal overgrowth comes at the expense of Treg populations (Bacher et al., 2014; Li et al., 2025). This imbalance creates a “proinflammatory bias,” where the host is less capable of resolving inflammation (Bacher et al., 2014; Li et al., 2025). This failure of the resolution mechanisms leads to sustained increases in the levels of cytokines (IL-6, TNF-α, IL-17) that are capable of compromising the BBB, thereby facilitating the infiltration of peripheral immune mediators into the brain and influencing neural function (Bacher et al., 2014; Choi et al., 2016; Gładysz et al., 2018; Li et al., 2025).

In summary, fungal dysbiosis in ASD may act as more than a localized mucosal irritant. Through the activation of the Syk–CARD9–NF-κB axis and the NLRP3 inflammasome, and the subsequent skewing of the Th17/Treg balance, fungal dysbiosis appears to be associated with systemic inflammatory pathology. However, whether fungal dysbiosis serves as a primary driver or a secondary amplifier of inflammation in human ASD requires confirmation through prospective longitudinal studies and interventional trials. This cascade provides a mechanistic bridge explaining how gut-resident fungi can drive the neuroimmune alterations, specifically microglial activation and synaptic dysfunction, implicated in the pathogenesis of ASD.

The human gut functions as a metabolic crucible where the resident microbiota synthesizes and modulates a vast array of neuroactive compounds (Caputi et al., 2021; Strandwitz, 2018). In the context of ASD, fungal dysbiosis—often co-occurring with bacterial imbalances—disrupts the production and homeostasis of these key metabolites (Averina et al., 2020; Pochakom et al., 2022). The resulting metabolic profile is characterized by the accumulation of neurotoxic byproducts and the depletion of neuroprotective factors. This section provides an in-depth analysis of the mechanistic pathways linking SCFAs, monoamine neurotransmitters, and fungal toxins to the neuropathology of ASD.

Critically, the disruption of these bacterial–fungal ecological dynamics, as detailed in section “2 Linking gut bacterial–fungal dysbiosis to systemic consequences,” fundamentally reshapes the metabolic landscape of the gut. As outlined previously, commensal bacteria are primary producers of key neuroactive metabolites, most notably SCFAs. The depletion of beneficial bacterial taxa, a hallmark of the dysbiotic state in NDDs, leads to a marked reduction in the production of metabolites like butyrate, which possesses neuroprotective and anti-inflammatory properties (Zheng et al., 2023). Concurrently, this bacterial dysbiosis erodes the competitive inhibition and immune-mediated containment that normally suppress fungal proliferation—a process ecologically defined as “niche release” (Gaspar et al., 2025; Severance et al., 2016). The resulting fungal expansion, particularly of opportunistic species like Candida, is not an isolated event but occurs within this altered metabolic milieu. Therefore, the effect of fungal dysbiosis within the context of this co-occurring bacterial dysbiosis and the resulting shifts in critical microbial metabolites must be examined to comprehensively understand the functional consequences of fungal dysbiosis. The following analysis of specific metabolites, including bacteria-derived SCFAs, is framed within this integrated pathophysiological model, wherein changes in the fungal community and the distorted metabolic output of the broader microbiota are inextricably linked drivers of pathology.

Elevated propionic acid (PPA) levels in ASD stool (Li et al., 2017; Wang et al., 2012) correlate with ASD-like phenotypes—hyperactivity, repetitive behaviors, and social deficits—following intraventricular administration in animal models. PPA crosses the BBB and enters neuronal cells (Chintharala et al., 2024). Once it enters cells, excess PPA accumulates in the mitochondria, where it sequesters carnitine to form propionyl-L-carnitine, leading to secondary carnitine deficiency (Fattorusso et al., 2019; Parellada et al., 2014; Thomas et al., 2010). This disruption impairs β-oxidation and the tricarboxylic acid (TCA) cycle, resulting in reduced adenosine triphosphate (ATP) production and altered neuronal energy metabolism (Fattorusso et al., 2019; Parellada et al., 2014; Thomas et al., 2010). Furthermore, PPA accumulation induces metabolic stress, generating reactive oxygen species (ROS) and depleting glutathione, which creates an oxidative environment that triggers the release of proinflammatory cytokines such as IL-6 and TNF-α (Thomas et al., 2010). These cytokines sensitize neuronal circuits and alter synaptic transmission, creating a foundation for neurobehavioral abnormalities (Benarroch, 2024; Vezzani and Viviani, 2015). Beyond these metabolic and oxidative stressors, PPA exerts direct and complex neuromodulatory effects that vary significantly with the kinetics of exposure. In chronic models involving direct central nervous system administration, such as repeated intracerebroventricular (ICV) infusions in rats, PPA modulates gap junction gating in regions like the striatum (MacFabe et al., 2007). This process is potentially driven by intracellular acidification, a consequence of the metabolic disruptions described above, which alters electrotonic coupling and calcium signaling (MacFabe et al., 2007). These changes are associated with increased neural excitability, as evidenced by epileptiform spiking in the hippocampus, cortex, and caudate nucleus (MacFabe et al., 2007). Such electrophysiological alterations coincide with specific behavioral abnormalities, including retropulsion, snake-like postures, turning, and limb dystonia, which contribute to the excitatory–inhibitory imbalance underpinning the hyperactivity and repetitive behaviors observed in ASD models (MacFabe et al., 2007). However, the neurochemical impact of PPA is not uniform and presents a dose-dependent dichotomy. In contrast to the excitatory profile of chronic exposure, acute systemic administration of PPA (e.g., intravenous injection) produces a divergent profile (Morland et al., 2018). Upon rapidly crossing the BBB, PPA is taken up by GABAergic neurons, where it acts as a potent inhibitor of mitochondrial GABA-T, with a K_i of approximately 1 mmol/L (Morland et al., 2018). This enzymatic inhibition leads to a rapid accumulation of intracellular GABA, enhancing vesicular packaging and release (Morland et al., 2018). The resulting increase in synaptic and extrasynaptic GABAergic tone suppresses cerebral glucose metabolism and overall neuronal excitability, manifesting behaviourally as lethargy and reduced activity rather than hyperactivity (Morland et al., 2018). Ultimately, the net effect of PPA on the excitatory–inhibitory balance in ASD is determined by the specific parameters of exposure. While the chronic, low-grade elevation in PPA levels typical of gut dysbiosis aligns closely with the gap junction modulation and mitochondrial stress pathways that drive network excitability and hyperactive behaviors, the potential for acute GABAergic inhibition highlights the complexity of the role of PPA in the gut-brain axis.

Butyrate is a major gut microbial metabolite that can act intracellularly as a HDAC inhibitor, with downstream effects on intestinal and systemic biology (Schulthess et al., 2019). In tissue-resident intestinal macrophages, butyrate induces an antimicrobial imprint that is predominantly linked to HDAC3 inhibition, rather than G-protein-coupled receptor (GPCR) signaling or broad suppression of cytokine transcription (Schulthess et al., 2019). This imprinting is associated with metabolic reprogramming that includes reduced mechanistic target of rapamycin (mTOR) activity and a shift toward altered glycolytic flux. This metabolic shift supports LC3-associated (microtubule-associated protein 1A/1B-light chain 3-associated) host defenses and the upregulation of antimicrobial effectors such as calprotectin (S100A8/S100A9) and other antimicrobial peptides (Schulthess et al., 2019). Importantly, the antimicrobial program can be activated with little or no increase in the levels of classical proinflammatory cytokines, indicating a decoupling of antimicrobial activity from overt mucosal inflammation in the gut mucosa (Schulthess et al., 2019). The HDAC-inhibitory action of butyrate is supported by studies showing that HDAC3 inhibition reproduces key antimicrobial phenotypes and that the effects of butyrate are diminished when HDAC3 expression is reduced or inhibited, placing HDAC3 upstream of the metabolic and antimicrobial reprogramming in macrophages (Schulthess et al., 2019). Chromatin-modifying changes consistent with HDAC inhibition include increased histone acetylation (e.g., Ac-H3 and Ac-H4) and coordinated transcriptional shifts toward antimicrobial/lysosomal programs, with limited increases in the levels of proinflammatory cytokines in this context (Schulthess et al., 2019).

Clinical metabolomic studies report reduced fecal butyrate levels and the depletion of key butyrate-producing taxa (e.g., Ruminococcaceae, Eubacterium, and Lachnospiraceae) in patients with ASD, suggesting diminished luminal butyrate signaling that could compromise intestinal barrier function and mucosal immunity, thereby influencing gut-brain axis signaling relevant to ASD phenotypes (Liu et al., 2019; Schulthess et al., 2019). This dysbiosis often involves a shift away from butyrate producers toward taxa associated with other SCFAs, potentially altering the balance of gut-derived immunometabolic signals that affect gut permeability and inflammation (Liu et al., 2019; Schulthess et al., 2019). The established mechanism by which butyrate, via HDAC3 inhibition, drives an antimicrobial and barrier-supportive program in macrophages without eliciting widespread proinflammatory cytokine production provides a plausible pathway through which ASD-associated reductions in butyrate levels could perturb local gut barrier integrity and immune homeostasis, thereby impacting gut-brain communication and neurodevelopmental trajectories (Chang et al., 2014; Liu et al., 2019; Schulthess et al., 2019).

Gastrointestinal serotonin synthesis is predominantly governed by enterochromaffin cells in the gut, and its magnitude is modulated by both tryptophan availability and microbial signals (Caspani et al., 2024). The current evidence consistently shows that changes in the gut microbiota in patients with ASD encompass not only bacterial dysbiosis but also alterations in the fungal component (mycobiota) (Yetgin, 2024). Although direct causal links between particular fungal taxa and central serotonin synthesis have not yet been established, fungus-derived signals may influence enteric serotonin production and peripheral 5-hydroxytryptamine (5-HT) levels indirectly through multiple pathways (Caspani et al., 2024). Fungal dysbiosis can, for example, impact gut barrier integrity, trigger mucosal immune responses with proinflammatory cytokines (IL-1β, IL-6, and TNF-α), and modulate tryptophan metabolism by affecting indoleamine 2,3-dioxygenase (IDO) activity, thereby shunting tryptophan away from serotonin synthesis toward the kynurenine pathway and altering the serotoninogenic milieu (Caspani et al., 2024; Kelly et al., 2017; Yetgin, 2024). Peripheral 5-HT levels in patients with ASD are inconsistent across studies. Since the 1970s, several reports have described hyperserotonaemia in patients with ASD (elevated 5-HT levels in whole blood or platelets) (Anderson et al., 1987; Fattorusso et al., 2019; Hanley et al., 1977; Minderaa et al., 1987), yet imaging studies suggest that the central serotonin synthesis capacity may be reduced during development in some children with ASD (hyposerotonemia) (Wang Q. et al., 2023). This apparent discordance highlights the complexity of the serotonergic system in individuals with ASD, potentially involving altered transport of the serotonin precursor (tryptophan) across the BBB, serotonin transporter (SERT) function, and genetic variations (e.g., SERT Ala56) that influence neuronal serotonin reuptake, as well as dysregulated feedback signaling from gut-derived serotonin to central circuits and the broader gut-brain feedback loops (Fattorusso et al., 2019; Kelly et al., 2017; Li et al., 2017; Wang Q. et al., 2023). Taken together, these factors imply that gut fungi are more likely to act as components of a broader, multikingdom regulatory milieu rather than as direct serotonin producers. Consistent with a multiomics framework, fungal dysbiosis interacts with co-occurring bacterial dysbiosis to reshape the gut metabolic landscape, including reductions in the abundance of beneficial SCFA-producing bacteria (e.g., butyrate producers), which may diminish the SCFA-driven stimulation of tryptophan hydroxylase 1 (TPH1) and constrain peripheral 5-HT production, thereby altering downstream serotonergic signaling implicated in ASD phenotypes (Fattorusso et al., 2019; Hadrich et al., 2024; Hughes and Ashwood, 2018; Kelly et al., 2017; Li et al., 2017, 2019; Strati et al., 2017; Wang Q. et al., 2023; Xiang et al., 2025). While these mechanistic inferences are biologically plausible and supported by associations among fungal composition shifts, immune activation, and SCFA metabolism, causal relationships remain to be established and should be validated in future studies using animal models, longitudinal designs, and interventional experiments.

With regard to dopamine, the existing literature suggests an indirect, ecosystem-level mode of regulation. Dysbiosis in individuals with ASD, including fungal overgrowth, may influence dopaminergic biosynthesis by affecting the host inflammatory state, the availability of precursors such as tyrosine, and the activity of key enzymes such as tyrosine hydroxylase (Fattorusso et al., 2019). Experimental models indicate that a chronic, gut-derived inflammatory environment can perturb dopaminergic circuits (Fattorusso et al., 2019). In addition, certain microbe-associated metabolites linked to dysbiosis may modulate dopaminergic signaling; for example, PPA has been shown to alter brain neurochemistry and mitochondrial function in animal models, potentially impacting dopamine pathways involved in rewards processing and motivation (Li et al., 2017; MacFabe et al., 2011). Although direct evidence demonstrating that gut fungal taxa regulate central dopamine synthesis in humans is limited, converging data from ASD microbiome studies imply that multikingdom interactions—bacteria and fungi—with host immune and metabolic responses may converge on the tyrosine–dopamine axis via inflammation, barrier integrity, and metabolite flux (Hadrich et al., 2024; Strati et al., 2017; Yetgin, 2024). Moreover, gut microbes [including fungi (Yetgin, 2024)] can itself produce neuroactive metabolites or neurotransmitter analogs (for instance, some bacteria produce dopamine precursors), although direct fungal evidence in this regard remains to be fully established (Li et al., 2017; Strandwitz, 2018; Wang Q. et al., 2023). Collectively, the current associative evidence supports a hypothetical model in which fungal dysbiosis may contribute to an altered gut-brain milieu that could indirectly influence dopamine synthesis in individuals with ASD, rather than acting as a direct neurotransmitter source. This proposed relationship requires validation through mechanistic studies and longitudinal observations. This interpretation awaits further validation of causality and the mechanism through integrated multiomics approaches, controlled animal models, and human interventional studies.

Beyond classical neurotransmitters, the gut mycobiome may contribute to the neurotoxic load in individuals with ASD through the production of specific metabolic byproducts. As previously described, the gut mycobiota in patients with ASD is often characterized by a well-documented increase in the abundance of Candida species, most consistently Candida albicans (Dargenio et al., 2023; Kantarcioglu et al., 2016; Zou et al., 2021). This fungal dysbiosis is notable because Candida species can release ammonia and other toxins, which have been hypothesized to contribute to autistic behaviors (Dargenio et al., 2023; Kantarcioglu et al., 2016; Li et al., 2017).

The finding of significantly higher fecal ammonia concentrations in children with ASD compared to controls provides a basis for proposing a role for ammonia in ASD. Elevated fecal ammonia levels may translate into higher systemic and brain ammonia levels, potentially contributing to neurotoxicity, but this hypothesis requires further investigation (Wang et al., 2012). Importantly, the elevated fecal ammonia level likely results from a combination of microbial sources and not solely from fungal dysbiosis. While Candida species, particularly C. albicans, which are frequently elevated in individuals with ASD, are hypothesized to release ammonia (Dargenio et al., 2023; Kantarcioglu et al., 2016; Wang et al., 2012; Zou et al., 2021), ammonia is also a major by-product of protein fermentation by gut bacteria (Wang et al., 2012). Furthermore, bacterial dysbiosis in patients with ASD often involves an increase in the abundance of specific bacteria such as Clostridium species, which are known producers of neurotoxic metabolites (Waligora-Dupriet et al., 2019). Therefore, the observed hyperammonaemia may stem from synergistic contributions of both bacterial and fungal dysbiosis. High colonic levels of ammonia have been shown to damage epithelial cells and increase gut permeability (Wang et al., 2012). Mechanistically, ammonia readily crosses the blood–brain barrier (Dasarathy et al., 2017). High brain ammonia levels (hyperammonaemia) are known to compromise astrocyte function (Dasarathy et al., 2017). A key neurotoxic mechanism involves the detoxification of ammonia in astrocytes, where it consumes α-ketoglutarate to generate glutamate and glutamine, leading to the depletion of tricarboxylic acid (Krebs) cycle intermediates and metabolic stress (Dasarathy et al., 2017). This mitochondrial dysfunction aligns with the broader concept of neuroinflammation. This neuroinflammatory state could be exacerbated by metabolic disturbances.

This neuroinflammatory state could be exacerbated by broader metabolic disturbances beyond the direct production of fungal toxins. Specifically, the intestinal dysbiosis characteristic of ASD extends to a disruption in the microbial synthesis of key neuroactive and immunomodulatory metabolites. This includes not only the previously discussed neurotransmitters and SCFAs, but also compounds such as GABA, biotin, and precursors to pivotal neuromodulators. Animal models of neurodevelopmental disorders support the link between gut dysbiosis and central neurotransmitter or synaptic dysfunction. For instance, studies using the maternal immune activation or BTBR mouse models of ASD have shown that gut dysbiosis leads to imbalances in tryptophan-derived metabolites (e.g., alterations in the serotonin and kynurenine pathways) and perturbs the glutamate-glutamine-GABA cycle, which are associated with behavioral abnormalities (Giuliano and Tognini, 2025; Wang X. et al., 2025). Furthermore, interventions such as fecal microbiota transplantation from patients to mice demonstrate that microbial alterations can directly influence behavior and associated neurochemical profiles (Wang X. et al., 2025). The intestinal fungal dysbiosis emphasized in this review likely exacerbates these deficits through converging pathways: by aggravating bacterial community disruption, it can compromise the bacterial microenvironment responsible for producing a balanced profile of neuroactive metabolites. For example, bacterial dysbiosis in ASD is linked to decreased production of neuroprotective metabolites like indole-3-propionic acid and kynurenic acid, while increasing pro-inflammatory molecules such as quinolinic acid (Giuliano and Tognini, 2025). Fungal dysbiosis, by driving bacterial ecological shifts, likely amplifies this imbalance. Thus, the impact of fungal dysbiosis converges mechanistically with broader neurotransmitter and synaptic abnormalities, operating within the “multihit” framework by disrupting the bacterial ecology essential for maintaining metabolic homeostasis.

Notably, current research cannot definitively determine a temporal sequence or a unidirectional causal relationship between mycobiota and bacteriobiota dysbiosis in individuals with ASD (Waligora-Dupriet et al., 2019). The existing evidence primarily indicates that these phenomena are frequently co-occurring and are likely interconnected, collectively contributing to the complex state of a destabilized gut ecosystem in affected individuals. The disturbance in bacterial communities (bacterial dysbiosis) may disrupt the microbial equilibrium, thereby fostering a permissive environment for fungal overgrowth (e.g., Candida spp.) (Waligora-Dupriet et al., 2019). Conversely, the proliferation of fungi may reciprocally alter the structure and function of the bacterial community. This bidirectional, potentially synergistic interaction underscores the complexity of multikingdom microbial dysregulation in ASD pathogenesis (Waligora-Dupriet et al., 2019).

Building upon the framework of bidirectional bacterial–fungal interactions, the pathophysiology of ASD can be further conceptualized as a “multihit” process (Parellada et al., 2014). This process is driven by a synergistic dysregulation of the multikingdom gut ecosystem, where fungal and bacterial dysbiosis are not sequential but co-occurring and mutually reinforcing (Parellada et al., 2014). In this model, fungal dysbiosis (e.g., Candida overgrowth) and bacterial dysbiosis (e.g., increased abundance of Clostridium species) collectively instigate a disrupted metabolic environment (Dargenio et al., 2023; Li et al., 2017; Strati et al., 2016; Waligora-Dupriet et al., 2019). While fungus-derived ammonia directly contributes to the neurotoxic load, its impact is synergistically magnified within a gut ecosystem concurrently reshaped by bacterial dysbiosis to favor the production of other harmful metabolites, such as PPA and phenolic compounds like p-cresol (Strati et al., 2016; Yetgin, 2024). Therefore, the interdependent dysregulation of both fungal and bacterial communities establishes a synergistic toxic environment in individuals with ASD. Concurrent exposure to elevated levels of PPA, ammonia, and p-cresol likely has compounded effects. Specifically, PPA-induced mitochondrial dysfunction and neuroinflammation could potentially render neurons more vulnerable to the excitotoxic effects associated with ammonia and the oxidative stress linked to other metabolites, illustrating the proposed “multihit” hypothesis in the context of ASD (Dasarathy et al., 2017; MacFabe et al., 2007; Parellada et al., 2014).

Critically, the neuropathological processes outlined in this “multihit” model—synaptic dysfunction, impaired neural circuit refinement, and neuroinflammation—are not exclusive to the core symptoms of ASD. They represent fundamental disruptions in brain development and function that are directly implicated in intellectual disability (ID), a condition that co-occurs in a significant subset of individuals with ASD and constitutes a major determinant of adaptive outcome (Alkuwaiti et al., 2025; Biagi et al., 2014). Therefore, the synergistic disruption of mitochondrial function, neuronal excitability, and neuroimmune homeostasis detailed above provides a plausible biological substrate for ID in the context of ASD. Specifically, disturbances in microbial-derived metabolites, such as reduced production of SCFAs like butyrate, may compromise epigenetic regulation of microglial and astrocyte function, processes critical for synaptic pruning and long-term potentiation (Han et al., 2025; Protic et al., 2025). In individuals with ASD and co-occurring ID, such multifactorial gut-brain axis dysregulation may be a key contributor to aberrant synaptic connectivity and the associated cognitive impairments.

Enteric fungal dysbiosis in individuals with ADHD is characterized by a notable enrichment of Candida species, most consistently Candida albicans, accompanied by phylum-level shifts favoring Ascomycota and a relative reduction in the abundance of Basidiomycota (Hadrich et al., 2024; Wang L. J. et al., 2023). This fungal imbalance is plausibly implicated in compromising intestinal mucosal barrier integrity, thereby contributing to a state of increased intestinal permeability known as a “leaky gut” (Hadrich et al., 2024; Iliev and Cadwell, 2021; Lionakis et al., 2023; Wang L. J. et al., 2023). In vitro data using Caco-2 cell monolayers indicate that filtrates or secreted products from C. albicans substantially increase epithelial barrier permeability, as evidenced by increased dye leakage and increased transepithelial flux of serum components (Wang L. J. et al., 2023). These findings imply that fungal secretions can disrupt the tight junction architecture and epithelial cytoskeleton, potentially via direct interference with tight junction proteins (e.g., occludin, claudins, and ZO-1) or through signaling cascades that drive cytoskeletal remodeling (Wang L. J. et al., 2023). Such barrier perturbations plausibly permit translocation of luminal MAMPs and fungal metabolites into the portal and systemic circulation, increasing the exposure of immune cells and hepatic surveillance systems to pathogenic fungal components (Leonardi et al., 2022; Lionakis et al., 2023; Wang L. J. et al., 2023). The consequence of this barrier breach is the systemic dissemination of fungus-derived molecules, such as β-glucans, and other metabolites (Lionakis et al., 2023). These circulating fungal ligands can serve as PAMPs that engage innate and adaptive immune receptors, eliciting a cascade of immune activation (Lionakis et al., 2023). Preclinical studies, primarily in mouse models, suggest a recurring theme of C-type lectin receptors (CLRs) such as Dectin-1, Dectin-2, and Dectin-3 on antigen-presenting cells recognizing fungal components (Iliev and Cadwell, 2021; Lionakis et al., 2023). In these models, receptor engagement triggers downstream signaling through Syk kinase and the CARD9–MALT1–BCL-10 axis, culminating in NF-κB activation and production of proinflammatory cytokines like IL-6, IL-23, and TNF-α (Iliev and Cadwell, 2021; Lionakis et al., 2023). In mouse models, this inflammatory milieu promotes the differentiation and expansion of CD4⁺ Th17 cells, along with the concomitant secretion of IL-17A and IL-22 (Leonardi et al., 2022; Lionakis et al., 2023). Studies in mice indicate that IL-22 contributes to mucosal defenses and epithelial renewal, whereas IL-17A exerts robust proinflammatory effects, including neutrophil recruitment (Leonardi et al., 2022; Lionakis et al., 2023). In the context of persistent fungal dysbiosis, a maladaptive Th17/IL-17 signaling balance is proposed to contribute to tissue injury and sustained barrier disruption (Leonardi et al., 2022; Lionakis et al., 2023).

Concurrent with barrier and immune mechanisms, fungal dysbiosis interacts with bacterial community dynamics to influence barrier integrity and neuroimmune signaling (Iliev and Cadwell, 2021). Preclinical evidence from mouse models suggests that certain bacterial taxa with barrier-supporting functions, such as certain Bacteroides spp. and Blautia spp., may promote barrier fortification through mechanisms like hypoxia-inducible factor (HIF-1α)-driven pathways and antimicrobial peptide production [e.g., cathelicidin-related antimicrobial peptide (LL-37)], thereby potentially restraining Candida colonization and stabilizing the mucosal milieu (Lionakis et al., 2023). Conversely, the overgrowth of Candida can perturb the bacterial community structure via resource competition, pH alterations, or the secretion of antifungal or antibiosis factors, potentially diminishing beneficial bacterial collaborators that support barrier integrity (Dalle et al., 2010; Deveau et al., 2018; Gaspar et al., 2025; Hadrich et al., 2024; Shuai et al., 2022; Strati et al., 2017; van Tilburg Bernardes et al., 2020). Interkingdom crosstalk thus represents a bidirectional regulatory axis in which expanded fungal communities and bacterial dysbiosis mutually reinforce each other, shaping the inflammatory tone and the pool of microbial metabolites, including SCFAs, which themselves modulate mucosal immunity and CNS function (van Tilburg Bernardes et al., 2020).

Building on the barrier disruption detailed in section “4.2.1 Effect of a fungal imbalance on the intestinal mucosal barrier,” fungal components such as β-glucans enter the circulation and engage C-type lectin receptors (e.g., Dectin-1/2/3) on immune cells (Lionakis et al., 2023). This interaction activates the Syk–CARD9–NF-κB axis, driving proinflammatory cytokine production (IL-6, IL-23, IL-1β, TNF−α) as described in section “3.2.2 Immune dysregulation and systemic inflammation” (Lionakis et al., 2023). Th17-derived IL-17A amplifies inflammation. Under persistent fungal exposure, this response shifts from protective to pathological, driving excessive systemic inflammation (Iliev and Cadwell, 2021; Leonardi et al., 2022; Lionakis et al., 2023; Zhang et al., 2025). Concurrently, the sustained inflammatory milieu further compromises epithelial barrier function. The disruption of barrier integrity, in turn, creates favorable conditions for fungal colonization and antigen exposure, which perpetuate the stimulation of Th17 immunity. This process establishes a self-amplifying, feed-forward loop that exacerbates both systemic inflammation and barrier impairment (Iliev and Cadwell, 2021; Leonardi et al., 2022; Lionakis et al., 2023; Zhang et al., 2025).

These translocated fungal ligands activate innate immune surveillance in hepatic and splenic networks (Leonardi et al., 2022; Lionakis et al., 2023). Human studies in ADHD cohorts link Candida enrichment to elevated systemic inflammatory markers and barrier dysfunction, supporting a gut–immune–brain axis despite causal limitations (Hadrich et al., 2024; Wang L. J. et al., 2023). IL-17A may act as a neuromodulator: rodent studies show fungus-induced IL-17A can influence social and reward-related behaviors via neuronal IL-17 receptors (Leonardi et al., 2022; Lionakis et al., 2023). However, translation to humans remains inferential and requires longitudinal confirmation.

Fungal overgrowth disrupts bacterial consortia, altering SCFA profiles and exacerbating inflammation (Leonardi et al., 2022; van Tilburg Bernardes et al., 2020). This crosstalk amplifies systemic inflammatory signals reaching the CNS via humoral (cytokines crossing BBB) and neural (vagal afferents) routes (Hadrich et al., 2024; Leonardi et al., 2022; Lewis et al., 2025), potentially modulating monoaminergic neurotransmission and executive functions relevant to ADHD (Checa-Ros et al., 2021).

These potential modulations of key neurotransmitter systems occur through specific mechanisms by which peripherally derived immune signals interface with the CNS. Proinflammatory cytokines such as IL-6, IL-1β, and TNF-α can access the CNS via several routes, including direct transit across a permeable or compromised BBB and signaling through circumventricular organs where the BBB is inherently leaky (Lewis et al., 2025). Within the CNS, these cytokines can modulate the synthesis, release, reuptake, and receptor sensitivity of monoamines—dopamine, norepinephrine, and serotonin—in prefrontal and subcortical networks critical for attention, working memory, and executive control (Lewis et al., 2025). For instance, IL-6 can influence tryptophan metabolism via the tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) pathways, potentially reducing central serotonin availability and generating neuroactive kynurenine metabolites that affect glutamatergic signaling and microglial activation (Checa-Ros et al., 2021; Lewis et al., 2025). TNF-α and IL-1β can alter dopamine transporter function and dopaminergic neuron firing in frontostriatal circuits, potentially shifting the balance between tonic and phasic dopamine signaling that underpins sustained attention and cognitive control (Borrajo et al., 2014; Channer et al., 2023; Felger and Lotrich, 2013; Goldsmith et al., 2023; Lee et al., 2018; Lewis et al., 2025; Lewitus et al., 2014; Miller et al., 2017). IL-1β can also modulate norepinephrine signaling in the prefrontal cortex, influencing the signal-to-noise ratio and executive performance (Lee et al., 2018). Collectively, these cytokine-driven changes can recalibrate frontostriatal dynamics and rewards processing, contributing to ADHD-related impairments in attention, working memory, inhibitory control, and susceptibility to distraction.

Following the modulation of key neurotransmitter systems, these peripherally derived immune signals extend their influence to synaptic plasticity and large-scale neural networks. Systemic inflammation can prime microglia, altering synaptic pruning, receptor expression, and dendritic spine dynamics within prefrontal and striatal circuits (Lewitus et al., 2014; Miller et al., 2017). These changes lead to desynchronized thalamocortical and cortico-striatal communication, disrupting the maturation and efficiency of critical networks like the default mode network and frontoparietal control systems, and thereby contributing to deficits in planning, cognitive flexibility, and response inhibition that are characteristics of ADHD (Bush, 2010; Checa-Ros et al., 2021; Goldsmith et al., 2023; Konrad and Eickhoff, 2010; McCarthy et al., 2014; Rubia et al., 2019). Concurrently, the integrity of the blood–brain barrier can be compromised by inflammatory mediators, facilitating the central entry of peripheral immune signals and altering the chemical milieu in the CNS via changes in tight junction proteins and transporter function (Channer et al., 2023; Felger and Lotrich, 2013; Goldsmith et al., 2023). This process further modulates monoamine availability in key regions such as the dorsolateral prefrontal cortex and anterior cingulate cortex (Boyle et al., 2024; Bush, 2010; Cools and Arnsten, 2022; Felger and Lotrich, 2013; Goldsmith et al., 2023; Lee et al., 2018; Miller et al., 2017). The peripheral inflammatory tone also interacts with gut-derived metabolites and vagal signaling. SCFAs and tryptophan-derived metabolites can influence CNS function via afferent vagal pathways, which in turn can rapidly adjust monoaminergic signalling and plasticity in attention and rewards networks, potentially exacerbating or mitigating ADHD-related symptoms (Checa-Ros et al., 2021; Lewis et al., 2025).

Collectively, the multi-level disruptions in neurotransmitter signaling, synaptic plasticity, and peripheral-CNS communication described above converge to compromise the integrated functioning of large-scale brain networks. The resultant inefficiency in frontostriatal and cortical networks directly undermines the cognitive domains of working memory, cognitive flexibility, and inhibitory control (Alkuwaiti et al., 2025). These executive functions constitute core pillars of general intellectual functioning, thereby linking the proposed gut-derived dysregulation to the cognitive deficits that are a hallmark of ADHD and can manifest as ID in more severe or co-morbid presentations (Alkuwaiti et al., 2025; Ramírez et al., 2022). Mechanistically, an altered gut microbiota can affect the availability of dopamine precursors (e.g., phenylalanine and tyrosine) and shift the balance of kynurenine pathway metabolites, both of which are critical for modulating prefrontal cortex-mediated executive processes (Alkuwaiti et al., 2025). Furthermore, a reduction in beneficial bacteria such as Faecalibacterium prausnitzii, which is associated with a pro-inflammatory state, may impair neuronal energy metabolism by diminishing mitochondrial support normally provided by microbial short-chain fatty acids, thereby exacerbating cognitive impairment (Protic et al., 2025).

In summary, an integrative, testable cascade can be proposed: intestinal fungal dysbiosis may lead to barrier disruption and the translocation of fungal components, which could trigger CLR–Syk–CARD9–NF-κB-mediated pro-inflammatory cytokine production and Th17/IL-17 response. This proposed mechanistic framework is grounded in well-established immunological pathways; however, its specific application to ADHD pathophysiology is primarily supported by associative human data (Leonardi et al., 2022; Lionakis et al., 2023). This process results in systemic inflammation whose signals, which are conveyed by humoral and neuronal pathways, promote CNS neuroinflammation, alter monoaminergic neurotransmission and synaptic plasticity in frontostriatal circuits, and ultimately yield neurobehavioral deficits consistent with the core symptoms of ADHD (Channer et al., 2023; Lee et al., 2018; Lewis et al., 2025). Notwithstanding this integrative cascade, establishing causality in humans remains challenging given the predominantly cross-sectional data, heterogeneity in mycobiome assessment methods, age ranges, ADHD subtypes, and medication statuses (Cassidy-Bushrow et al., 2023; Checa-Ros et al., 2021; Hadrich et al., 2024; Lewis et al., 2025; Wang L. J. et al., 2023). Furthermore, the interkingdom context adds another layer of complexity, as protective bacterial taxa can temper Th17 responses and promote anti-inflammatory SCFA production, whereas fungal overgrowth can tilt the balance toward proinflammatory signaling; disentangling direct fungal effects from those mediated by bacterial dysbiosis and metabolite shifts is therefore essential (Hadrich et al., 2024; Iliev and Cadwell, 2021; Lewis et al., 2025; Lionakis et al., 2023; van Tilburg Bernardes et al., 2020). While animal work provides a coherent mechanistic link between fungal IL-17 signaling and neural outcomes, human confirmation is still associative, and longitudinal multiomics studies are needed to establish temporality and causality and to delineate ADHD-specific neurobiological readouts. Thus, while the proposed mechanistic framework is grounded in well-established immunological pathways, such as the CLR–Syk–CARD9–NF-κB signaling axis, its specific application to ADHD pathophysiology is primarily supported by associative human data (e.g., studies linking Candida-dominant mycobiomes to intestinal permeability) (Lionakis et al., 2023; Wang L. J. et al., 2023). Therefore, in areas where direct human ADHD evidence is limited, the claims should be framed as plausible links awaiting causal substantiation, with an explicit acknowledgment of methodological heterogeneity and translational gaps (Cassidy-Bushrow et al., 2023; Checa-Ros et al., 2021; Lewis et al., 2025; Lionakis et al., 2023; Wang L. J. et al., 2023).

The pivotal genetic defect in RTT, loss-of-function mutations in the methyl-CpG-binding protein 2 (MeCP2) gene, extends beyond the central nervous system to fundamentally alter the gastrointestinal environment, thereby creating conditions conducive to microbial dysbiosis (Strati et al., 2016). MeCP2 has been shown to be a critical regulator of several interconnected systems within the gut, and its impairment contributes to a pro-dysbiotic niche through three primary mechanisms: disruption of the enteric nervous system (ENS), compromise of the mucosal barrier, and dysregulation of neuroimmune pathways (Cordone, 2024; Strati et al., 2016). Specifically, MeCP2 is expressed in the ENS, and its dysfunction is directly implicated in the disordered gut motility characteristic of RTT, leading to diminished gastrointestinal regulation, an increased intestinal transit time, and chronic constipation—a symptom that has been reported in more than 70% of RTT patients (Cordone, 2024; Strati et al., 2016). Consequently, this costive gut environment alters microbial colonization dynamics by extending the retention of luminal contents, which favors the proliferation of a dysbiotic microbial community adapted to these conditions (Cordone, 2024). Importantly, recent evidence indicates that disruption of the gut microbiome, particularly the depletion of butyrate-producing Clostridia species, reduces butyrate production leading to epithelial oxygenation, thereby disrupting the mucosal hypoxic environment that normally limits Candida growth and promoting C. albicans expansion (Deveau et al., 2018; Marsaux et al., 2025; Mishra and Koh, 2024). This mechanism is particularly relevant in the context of RTT-associated dysbiosis, where alterations in bacterial community composition may compromise the anaerobic conditions that maintain colonization resistance against facultative anaerobic fungi. Furthermore, the integrity of the gut’s mucosal barrier is compromised, as impairments in MeCP2 function are hypothesized to affect the regulation of genes essential for maintaining the protective mucus layer secreted by goblet cells (Cordone, 2024; Strati et al., 2016). These changes can lead to a reduction in the mucin layer, weakening the physical barrier that segregates luminal microbes from the host epithelium and predisposing the gut to colonization by opportunistic pathobionts, such as Candida and Escherichia/Shigella, whose translocation contributes to systemic inflammation (Strati et al., 2016, 2018; Yadav et al., 2024). Notably, fungal pathogens exhibit distinct colonization advantages in this compromised mucosal environment. Candida species express adhesins (such as Als proteins) that facilitate adherence to exposed epithelial surfaces when the mucin barrier is diminished (Liu et al., 2025). Moreover, the thinning of the mucus layer reduces the physical barrier that separates luminal fungi from the host epithelium. Importantly, mucins and mucin O-glycans within the mucus layer act as natural inhibitors of Candida albicans pathogenicity by suppressing filamentation-associated gene expression and blocking the yeast-to-hyphal transition (Liu et al., 2025; Takagi et al., 2022). Therefore, mucus layer depletion not only facilitates fungal access to epithelial surfaces but also removes the suppressive effects of mucin glycans on fungal morphological switching, thereby promoting the transition from commensal yeast forms to invasive hyphal forms—a transition critical for tissue invasion and pathogenicity (Liu et al., 2025; Takagi et al., 2022). The compromised barrier also permits bidirectional exchange of metabolites and signaling molecules between fungi and host immune cells, potentially accelerating the transition from mutualistic fungal colonization to pathogenic overgrowth (Allert et al., 2018; Sprague et al., 2024).

Lastly, MeCP2 mutations disrupt the tightly regulated neuroimmune network, causing an inadequate or dysregulated immune response at the mucosal surface (Cordone, 2024). MeCP2 deficiency has been shown to influence cytokine regulation, affecting Th1/Th17 and Treg cell balance (Gładysz et al., 2018; Hernández-Santos and Gaffen, 2012; Leoncini et al., 2015; Strati et al., 2016). The dysregulated immune environment in RTT is characterized by altered Th1/Th2/Th17 responses, with elevated pro-inflammatory cytokines contributing to a subclinical inflammatory state (Gładysz et al., 2018; Leoncini et al., 2015; Strati et al., 2016). While Th17 cells and their cytokine products (IL-17 and IL-22) are essential for maintaining epithelial barrier integrity and coordinating antifungal immunity, the precise impact of MeCP2 deficiency on these specific antifungal defense mechanisms in RTT remains to be fully elucidated (Aggor et al., 2020; De Luca et al., 2010; Napoli et al., 2025; Zelante et al., 2009). Furthermore, MeCP2 deficiency-linked immune dysregulation could potentially compromise antifungal effector pathways (including those dependent on neutrophil activity), thereby diminishing fungal clearance and permitting persistent colonization by Candida and other fungal taxa (Caputi et al., 2024; Gonçalez et al., 2024; Sparber and LeibundGut-Landmann, 2019; Strati et al., 2016; Zelante et al., 2009). To date, no studies have directly and rigorously demonstrated a causal relationship between MeCP2 deficiency and impaired neutrophil phagocytosis, killing, or fungal clearance activity, representing an important area for future investigation.

The intimate coexistence of bacterial and fungal communities suggests that perturbations in the bacteriome can significantly influence the mycobiome (Strati et al., 2016). In patients with RTT, the characteristic loss of bacterial diversity, often involving a decrease in the abundance beneficial commensals and an overabundance of potentially proinflammatory taxa, is a key factor contributing to fungal dysbiosis (Strati et al., 2016). This process unfolds through several interconnected mechanisms. First, the reduced abundance of a healthy commensal population compromises competitive exclusion, thereby freeing up essential nutrients, such as simple carbohydrates, and physical adhesion sites on the intestinal mucosa that fungi like Candida can exploit (Iliev and Leonardi, 2017). Second, the depletion of specific bacterial taxa, such as Lactobacillus and Bifidobacterium, diminishes the direct inhibition of fungal growth (Strati et al., 2016). This loss is critical, as these bacteria are known to produce antifungal compounds, including bacteriocins and SCFAs, that can disrupt fungal cell membranes or interfere with quorum-sensing signals necessary for virulence (Iliev and Leonardi, 2017). Consequently, the RTT-associated alterations in these populations create a more permissive environment. Furthermore, the altered metabolic output of the dysbiotic community can actively support fungal proliferation through metabolic crosstalk (Zhang et al., 2022). For instance, shifts in bacterial fermentation can result in the production of metabolites like specific amino acids or alcohols that serve as alternative nutrient sources for Candida, or they can alter local environmental conditions, such as pH and oxygen tension, to favor fungal growth and morphogenesis (Zhang et al., 2022). Collectively, the erosion of bacterial competition, the loss of direct antifungal inhibition, and the establishment of a supportive metabolic niche create conditions that facilitate the overgrowth of opportunistic fungi such as Candida (Iliev and Leonardi, 2017; Jiang et al., 2020; Yadav et al., 2024).

A key metabolic feature of the gut environment of patients with RTT is the abnormal accumulation of specific SCFAs, with studies consistently showing significantly elevated fecal levels of propionate, isobutyrate, and isovalerate in affected individuals (Borghi and Vignoli, 2019; Cordone, 2024; Strati et al., 2016). These dysregulated microbial metabolites are implicated as key contributors to local gut pathophysiology through two interconnected mechanisms. First, high concentrations of SCFAs are known to inhibit colonic motility presumably through mechanisms such as the SCFA-mediated release of peptide YY (PYY) from enteroendocrine cells, which in turn suppresses smooth muscle contractions (Strati et al., 2016). Consequently, this impaired motility contributes directly to the chronic constipation prevalent in patients with RTT, prolonging the intestinal transit time and thereby reinforcing the dysbiotic microbial community by extending its exposure to retained luminal contents (Cordone, 2024; Strati et al., 2016). Second, these elevated SCFA levels can disrupt the integrity of the mucosal barrier by interfering with the normal exocytosis of mucins from goblet cells (Strati et al., 2016). This compromise in barrier function leads to a reduction in the protective mucin layer, which facilitates the translocation of pathobionts like Candida and Escherichia/Shigella across the epithelium and contributes to the low-grade systemic inflammation observed in patients with RTT (Strati et al., 2016; Yadav et al., 2024). Beyond the gut, these SCFAs exert broad systemic effects that may intersect with the neurodevelopmental pathology of RTT (Borghi and Vignoli, 2019). As signaling molecules, SCFAs, particularly propionate and butyrate, can modulate host gene expression (potentially via HDAC inhibition), influence neurotransmitter systems, and affect mitochondrial function (MacFabe, 2015; Nankova et al., 2014; Strati et al., 2016). Therefore, the altered SCFA profile in individuals with RTT may represent a critical mechanistic link between gut dysbiosis and the systemic manifestations of the disorder, including both gastrointestinal dysfunction and potential contributions to neuroinflammation and behavioral phenotypes.

A compromised mucosal immune response in individuals with RTT represents a critical factor in the shift from fungal commensalism to pathogenic overgrowth (Strati et al., 2018). This immune dysfunction manifests as a subclinical inflammatory status within the gastrointestinal tract, as evidenced by elevated levels inflammatory markers, including fecal calprotectin, erythrocyte sedimentation rate (ESR), and serum IgA (Strati et al., 2016). This low-grade inflammation is likely instigated by the translocation of microbial components through a compromised mucosal barrier, which in turn triggers a dysregulated immune response (Cordone, 2024). The underlying genetic defect in RTT directly impacts immune function, as MeCP2 is a known epigenetic regulator of immune and inflammatory responses that plays a critical role in the differentiation and function of Th cells (Strati et al., 2018). Specifically, MeCP2 deficiency is implicated in the impaired regulation of Th1 and Th17 cell lineages—pathways essential for mounting an effective antifungal defense at mucosal surfaces (Strati et al., 2018). Consequently, the mucosal immune system is less capable of controlling fungal populations (Strati et al., 2018). This impairment is compounded by aberrant cytokine profiles; for instance, while innate immune cells produce elevated levels of pro-inflammatory cytokines like IL-1β in response to Candida isolates from RTT patients, they also induce the production of the immunosuppressive cytokine IL-10 at significantly higher levels (Strati et al., 2018). Such a dysregulated cytokine environment, characterized by non-resolving inflammation, can impair fungal clearance and promote microbial persistence (Strati et al., 2018). In this permissive niche, opportunistic fungi like Candida parapsilosis can transition to pathogenic forms, exhibiting enhanced virulence-related traits such as increased biofilm formation and resistance to antifungals, thereby perpetuating the cycle of inflammation and dysbiosis characteristic of RTT (Cordone, 2024; Strati et al., 2018).