The gut microbiome plays a crucial role in maintaining human health and contributing to disease pathogenesis^[1]. It is a highly diverse and dynamic microbial community of bacteria, viruses, fungi, and archaea that populate the gastrointestinal (GI) tract^[2,3]. The microbes regulate a variety of physiological processes, such as immunological regulation, metabolism, and digestion, that maintain overall homeostasis^[4,5]. Metabolites derived from the gut regulate behavior, emotion, and cognition, and are central regulators of immunological responses, systemic inflammation, metabolic disorders, and neurological function^[6,7]. There are a variety of factors that influence gut microbiota composition, such as age, sex, diet, environment, and genetics^[8].

Dysbiosis is a disruption of the gut microbiota that leads to metabolic disease and has also been implicated in immune activation and systemic inflammation^[9]. In human and animal models, gut dysbiosis research has investigated immunological dysregulation, brain protein aggregation abnormalities, and reduced neuronal and synaptic activity, which are key drivers of neurodegenerative diseases^[10]. Advances in gut microbiome research have unveiled the broad-ranging influence of gut microbiota on immuno-metabolism and brain health, and unearthed sophisticated interactions between microbial communities and host physiology^[11-13].

Alterations in gut microbial composition and the metabolites they produce are involved in regulating metabolism and controlling liver and brain function^[14,15]. The gut-liver barrier regulates the gut-liver interaction; upon passage, bacteria and their metabolites become accessible to the liver and contribute to a variety of hepatic ailments^[16]. In addition, stimulation of vagal and spinal afferent neurons by intestinal-derived peptides and hormones released in response to eating affects neuronal signaling, modulating gut and liver function through parasympathetic regulation^[17]. The gut-liver-brain axis is a multifaceted communication pathway that involves all three organs, regulating immunological, hormonal, metabolic, and neurological signals^[18,19]. The intricacy of microbial communities, which collectively have 100-fold more genes than the human genome, and their interactions with human physiology have been an active area of research in recent years^[20].

Gaucher disease (GD) is a rare autosomal recessive disorder characterized by reduced lysosomal β-glucocerebrosidase (GCase) activity resulting from mutations in the GBA1 (Glucosylceramidase Beta 1) gene on chromosome 1 (1q21). Ninety percent of disease-causing alleles in GBA1 gene are attributed to four most common variants: c.1226A>G (N409S or N370S), c.84dupG (84GG), c.1448T>C (L483P or L444P), and c.115+1G>A (IVS2+1)^[21,22]. Deficiency of GCase leads to excessive storage of glucocerebrosides in lysosomes, predominantly in the macrophages, described as lipid-rich macrophages, known as Gaucher cells^[23,24]. The most common clinical manifestations of GD include hepatosplenomegaly, anemia, thrombocytopenia, bone pain, and skeletal abnormalities due to the accumulation of Gaucher cells in organs, causing abdominal distension and tenderness, asthenia, bleeding tendencies, and immune dysfunction^[25,26]. Bone complications in GD, such as pain, osteopenia, fractures, and avascular necrosis, are severe and significantly affect the quality of life of patients with GD^[27].

The commonly recognized phenotypic forms of GD are Type 1 (non-neuronopathic), Type 2 (acute neuronopathic), and Type 3 (chronic neuronopathic) [Table 1]. Type 1 is the most frequent, constituting 95% of all GD, with a median age at diagnosis typically in adulthood. Type 2 appears during infancy with severe neurological impairment and is usually fatal during the initial years of life. Type 3 is chronic, with progressive neurological deterioration, which is slower compared to Type 2^[28,29]. The worldwide prevalence of GD1 is 0.9 (95%CI: 0.7-1.1) per 100,000 individuals. Latin America has the lowest prevalence estimates (0.15-0.32), followed by the Middle East (0.20-0.33, excluding Israeli values), Europe (0.11-1.1), and North America (0.60-1.93)^[30]. Ashkenazi Jews have a higher risk of GD1, particularly associated with the c.1226A>G and c.84dupG variants. In contrast, individuals carrying the c.1448T>C variant have an increased risk of developing neurological complications, commonly seen in patients with GD2 and GD3^[22].

GBA1 gene variants lead to specific molecular changes that trigger a series of signaling pathways, including oxidative stress, endoplasmic reticulum (ER) stress, mitochondrial dysfunction, inflammation, immune activation, and defects in autophagy and extracellular vesicle production^[31]. Autophagy, a key regulator of cellular homeostasis, is strongly influenced by the gut microbiota. Dysbiosis has been associated with impaired lysosomal function and disruption of the gut and blood-brain barrier (BBB) integrity, triggering neuroinflammation through alterations in microglial and regulatory T-cell activity, ultimately promoting protein misfolding and neurodegeneration. Further, Restorative Microbiota Therapy (RMT), including probiotics, prebiotics, synbiotics, and Fecal Microbiota Transplantation (FMT), has been proposed as a strategy to restore eubiosis, immune balance, and autophagic function in neurodegenerative diseases^[32,33], but it requires further validation in animal models and clinical studies.

The heterozygous GBA1 variant is the most common genetic risk factor for PD, implicating lysosomal dysfunction in neurodegeneration^[34]. Emerging evidence also suggests that gut microbial dysbiosis may contribute to PD via the gut-brain axis, promoting systemic inflammation, microglial activation, and lysosomal stress^[35]. PD is believed to include a prodromal phase characterized by GI dysbiosis, suggesting that microbial changes may precede overt neurological comorbidities. However, it remains challenging to establish whether dysbiosis is a precursor to or a consequence of PD^[36].

Traditionally, GI manifestations have not been a major focus in GD management, apart from reports of early satiety due to highly enlarged spleens^[37]. Despite the well-characterized systemic manifestations of GD, the role of gut dysbiosis remains under-investigated. However, recent pre-clinical studies [Table 2] of GBA1 gene variants indicate that the gut may play a pivotal role in GD pathophysiology and contribute to the phenotypic heterogeneity observed in GD.

This review highlights preclinical evidence of GBA1-associated gut dysbiosis and describes potential microbiome-mediated pathways that may contribute to the pathogenesis of GD and associated complications. To date, no clinical studies have systematically characterized the gut microbiome in patients with GD; current knowledge is limited to preclinical GBA1-based models in Drosophila and mice, as well as insights drawn from related complications. The novelty of this work lies in (i) integrating immune-metabolic, skeletal, and neurological perspectives within a single microbiome-focused framework specific to GD; and (ii) translating these preclinical observations into a hypothesis-driven clinical framework [Figure 1], with all proposed mechanisms considered exploratory and warranting further research alongside established GD therapies.

The human gut microbiota comprises a complex and dynamic network of trillions of microorganisms, including bacteria, viruses, fungi, archaea, and protozoa, with the majority residing in the GI tract. Microbes play a crucial role in various physiological processes, including immune system regulation, digestion, metabolism, and neurological function^[2]. Numerous factors, including age, diet, environment, genetics, lifestyle, geography, and antibiotic therapies, influence the gut microbiome. These factors collectively determine the composition and function of the gut microbiota, which are crucial to overall human health^[3,38].

GD is linked with multi-systemic complications. The manifestations include hepatosplenomegaly, anemia, thrombocytopenia, and a variety of skeletal issues, such as osteopenia, lytic lesions, fractures, chronic bone pain, bone crisis, bone infarction, osteonecrosis, and skeletal deformities^[58]. Patients with GD are at an increased risk of developing PD compared to the general population^[59]. It has been shown that microbial metabolites, such as increased bacterial lipopolysaccharides (LPS) and decreased SCFAs, can affect neuroinflammation and dopaminergic neuronal degeneration, which are essential events in the pathogenesis of PD^[60]. GI complications are rarely reported in GD and typically occur in patients with more severe phenotypes^[61]. As a result, available reports are primarily limited, most often involving neuronopathic variants. In the context of GD, it is plausible that GBA1 gene variants are associated with gut microbial alterations, suggesting that microbiome-targeted strategies may be conceptually informative for understanding disease heterogeneity. However, direct clinical evidence supporting such approaches in GD is currently lacking.

Despite the absence of direct clinical evidence in GD, preclinical GBA1 models suggest gut dysbiosis may be associated with complications via immune activation, barrier dysfunction, and metabolite dysregulation [Table 2]. These findings are hypothesis-generating and require validation in well-controlled human GD cohorts, where confounders such as enzyme replacement therapy (ERT)/substrate reduction therapy (SRT) status, diet, and antibiotics must be prospectively controlled.

To date, evidence of gut dysbiosis in GD has been derived exclusively from GBA1-based animal models. No human clinical studies examining the gut microbiome in GD have been reported. Consequently, these preclinical findings form the primary basis for hypothesizing a role for the microbiome in the pathophysiology of GD. However, species-specific differences between mice and humans must be carefully considered when interpreting and extrapolating these results^[84]. Studies in Drosophila and murine models carrying GBA1 variants revealed the role of gut dysbiosis in these pathologies. In Drosophila models of GD, deleting the GBA1 gene has been shown to significantly disrupt gut microbiome composition, leading to pronounced gut dysbiosis. This microbial imbalance is associated with increased intestinal permeability and an enhanced innate immune response, highlighting a breakdown in intestinal homeostasis^[85]. Another study in Drosophila with either the D370S or L444P variant showed that D370S caused more severe lysosomal dysfunction in the gut. In contrast, the L444P variant caused damage to brain cells^[86]. In a mouse PD model, heterozygous A53T-L444P mice exposed to environmental stressors showed gut dysbiosis and cognitive impairments. PD-related symptoms appeared only in A53T-L444P mice. These changes were linked to a loss of Lactobacillus sp. and altered behavior, suggesting a key role for the gut microbiome in neurodegeneration^[87]. In another mouse model with GBA1 L444P heterozygous variants, it has been suggested that GBA1 mutations alone may not be sufficient to cause gut dysbiosis. However, longitudinal studies have shown that the GBA1 L444P/WT mouse model does experience a microbial imbalance. This imbalance was associated with systemic inflammation and altered metabolism^[88]. These studies, summarized in Table 2, reflect the clinical complications of GD and advanced PD.

Recent studies also highlight that gut dysbiosis plays a central role in maintaining intestinal barrier integrity and regulating systemic inflammation, which can lead to neurological, metabolic, and GI dysfunction^[89,90]. This can further exacerbate bone conditions, such as osteopenia and fractures, highlighting the potential relevance of gut microbial balance in the context of GD pathophysiology^[91].

These findings highlight the potential role of gut dysbiosis in the pathogenesis of GD-associated complications and underscore the need for further research to explore the underlying mechanisms that may be relevant to overall health in patients with GD. Therefore, the hypothesis that reestablishing microbial balance can represent a conceptual framework for future adjunctive strategies, pending rigorous preclinical and clinical validation.

Pertinently, distinguishing cause from consequence is essential. We therefore recommend conducting systematic gnotobiotic transfer experiments, in which germ-free mice are colonized with feces from GBA1-mutant donors versus controls, to determine whether GD-associated microbiota can transmit systemic inflammation, neuroinflammatory signatures, and bone phenotypes. Conversely, colonization of mutant mice with healthy humanized microbiota or defined consortia will test reversibility.

Stool sample collection is the most practical and widely used approach for evaluating gut microbiota, both for clinical and research purposes, as it is sufficient to assess the dense and diverse microbial communities. It is non-invasive, patient-friendly, and can be performed at home using standardized collection kits^[92]. Patients are instructed to refrigerate or freeze the sample before submitting it to the laboratory for analysis, typically within 24 h of collection. Techniques such as 16S rRNA (ribosomal RNA) gene sequencing and shotgun metagenomics are then employed to characterize microbial composition and function^[93,94]. It is crucial to remember that stool samples may not accurately reflect the microbiome of the upper GI tract (e.g., the small intestine), where microbial populations vary widely in density and composition. Instead, they represent the luminal microbiota of the distal gut. More invasive sampling techniques, including endoscopic biopsies, luminal brushing, and aspirated intestinal fluid, may be considered if upper gut involvement is suspected or if further study is required. However, these techniques are usually only used for research purposes because of their procedural complexity^[95]. A comprehensive clinical evaluation should accompany microbiota sampling to enhance the interpretability of results. Clinicians should assess GI symptoms such as bloating, early satiety, constipation, diarrhea, and abdominal discomfort^[96].

During clinical visits, standardized symptom questionnaires can help document bowel patterns in patients with GD. It is also essential to consider other factors, such as diet, antibiotic use, and GD therapies, as they have a significant impact on gut microbial dynamics. However, in family-based studies, collecting samples from first-degree relatives or cohabiting family members, such as parents or siblings, can offer valuable insights into the interplay of genetic predisposition and shared environmental exposures on microbiome composition in patients with GD. Integrating gut microbiota analysis into research protocols may provide deeper insight into GI symptoms and inform the design of microbiome-targeted research studies. A pragmatic, initial biomarker panel should include fecal SCFAs such as acetate, propionate, butyrate; fecal calprotectin and zonulin; and shotgun stool metagenomics; serum lyso-GL1; and a systemic inflammatory cytokine panel. These assays capture microbial function, gut barrier integrity, and disease burden and are suitable for longitudinal, within-person analyses.

If gut dysbiosis is shown to play a causal role in GD pathogenesis, interest in RMT as an investigational approach would increase. In addition to traditional GD indicators such as lyso-GL1 and Chitotriosidase^[97]. Several surrogate biomarkers can be employed to monitor the impact of RMT for patients with GD, such as monitoring SCFAs (butyrate, acetate, and propionate) that demonstrate the action of beneficial gut bacteria^[98]. Calprotectin and zonulin are markers of intestinal inflammation and barrier permeability, and their levels in both serum and fecal samples are elevated in individuals with PD^[99]. This may be useful for exploratory monitoring in future interventional studies in GD research. The low levels of the gut bacterium Faecalibacterium are linked to conditions such as IBD, colorectal cancer, and depression. Due to its role in supporting gut health, Faecalibacterium is being explored as a promising new probiotic therapy^[100]. Therefore, therapies such as probiotics, prebiotics, synbiotics, dietary, and lifestyle interventions are discussed here as investigational strategies with a mechanistic rationale, rather than established therapeutic options. Here, we discuss the conceptual rationale for these approaches in the context of GD pathophysiology and disease complexity. RMT holds mechanistic promise but carries particular safety concerns for patients with GD with immune alterations, including splenectomized individuals. Therefore, any clinical RMT program should follow a staged pathway, beginning with preclinical safety in relevant models, followed by Phase I safety trials with rigorous donor screening, and only then planning randomized efficacy trials.

Studying the gut microbiome in patients with GD presents unique challenges, as lifestyle, diet, and medications can independently influence microbial composition, regardless of disease status. Preclinical studies must account for factors such as coprophagy and housing conditions in mice to ensure reproducible results^[118,119]. Dysbiosis should be verified in both human donors and recipient animals following fecal microbiota transplantation to gain mechanistic insight into host-microbe interactions.

Emerging ecological frameworks offer a more holistic approach to evaluating microbiome changes^[120], and in some contexts, community stability may be more informative than the abundance of individual taxa^[121]. Machine learning methods, including random forest regression, can identify potential biomarkers, yet these findings require careful interpretation, given the need for large sample sizes, cross-validation, and mechanistic follow-up.

The low prevalence of GD further complicates the identification of robust, replicable microbiome signatures, limiting sample sizes. Longitudinal, intra-individual study designs are therefore essential, as they allow each individual to serve as their own control and enable intra-individual tracking of biomarkers before, during, and after interventions. These designs help control for clinical heterogeneity and treatment effects, while minimizing inter-individual variability, for instance, by collecting samples at consistent intervals or from individuals within the same household or under similar environmental conditions.

We propose a hypothesis-driven pilot clinical framework [Figure 1] that emphasizes longitudinal, intra-individual follow-up to investigate the link between the microbiome and GD. This includes patients naive to GD and those treated, GBA1 carriers, and healthy controls, with serial stool and plasma sampling at baseline, 6-12 months, and key treatment milestones (ERT/SRT initiation) coupled to integrated microbiome and metabolomic analyses. Participants should be stratified by GD type, treatment-naïve versus treated status, and splenectomy. Unavoidable confounders, such as recent antibiotics or significant dietary changes, should be documented systematically. Cross-sectional studies are discouraged due to high inter-individual variability.

This hypothesis-driven framework can identify gut microbial alterations associated with GD and generate testable hypotheses regarding disease mechanisms. However, causal inference will require further mechanistic or extended longitudinal studies. While identifying specific microbial species linked to GD complications may inform future research directions, any clinical translation remains premature at this stage. It could inform the development of adjunct microbiome-targeted therapies and diagnostic tools, ultimately improving outcomes for individuals with GD.

Looking ahead, the trajectory of this field can be envisioned across short-, medium-, and long-term goals. In the short term (1-3 years), robust, standardized pilot cohorts are needed to define reproducible microbiome signatures in GD and establish correlations with established biomarkers such as lyso-GL1 and systemic inflammatory mediators. Small randomized controlled trials may be considered to evaluate the safety and biomarker effects of probiotics, synbiotics, or dietary interventions. Over the medium term (3-6 years), validated biomarker panels predictive of disease progression, including prodromal neurological features such as Parkinsonism or skeletal complications, will be critical, alongside the development of defined microbial consortia as therapeutics to replace less controlled interventions such as FMT. Integration with existing GD registries can accelerate recruitment and ensure standardized data collection, thereby enhancing the overall effectiveness of the process. In the long term (6+ years), the goal is to develop precision adjunctive microbiome-based therapies tailored to an individual’s microbiome and metabolome profile, used in combination with ERT or SRT. If causal relationships are firmly established, such approaches may eventually help clarify mechanisms underlying symptom burden and disease heterogeneity, particularly in neurological and skeletal manifestations of GD.

Gut dysbiosis is descriptively associated with metabolic, immunological, and neurological processes that may be relevant to GD-related complications. Preclinical GBA1 models link dysbiosis with chronic immune activation, lysosomal abnormalities, and autophagic dysfunction. However, these findings remain correlational and model-dependent. Adjunct microbiome-targeted strategies provide a conceptual framework for biomarker discovery and hypothesis generation, rather than immediate clinical application. They may help identify novel candidate biomarkers for early diagnosis and prognosis, thereby informing future research directions relevant to patient-centered outcomes in GD. We propose consideration of an international GD-microbiome working group to harmonize sampling and share data.