Spinal pain (SP) manifests as a prevalent symptom in various spine-related disorders, encompassing neck pain (NP) and back pain (BP), further categorized into thoracic spine pain (TSP) and low back pain (LBP). The prevalence in the general population is noteworthy, with NP affecting approximately 44%, TSP 15%, and LBP 56% (Manchikanti et al., 2004). The impact of SP on daily life and occupational functions surpasses that of other musculoskeletal disorders due to the spine’s role as the central axis and core support of the human skeleton (Haldeman et al., 2012). The 2015 Global Burden of Disease study underscored SP as a paramount contributor to disability globally, especially affecting individuals aged 25–64 (GBD 2015 Disease and Injury Incidence and Prevalence Collaborators, 2016). Consequently, healthcare costs for SP treatment soared, reaching an estimated $134.5 billion in the United States in 2020 (de Luca et al., 2023). The pressing need for effective prevention and treatment strategies for SP is a critical concern in the realm of global public health.

The gut microbiota, comprising over 10 trillion microorganisms, exists harmoniously within the human intestinal tract, outnumbering human cells tenfold (Clark and Coopersmith, 2007; Zhang et al., 2015). The colon, serving as the primary habitat, hosts an astounding 10^∧11–10^∧12 microorganisms per milliliter (Ley et al., 2006). This rich, diverse, and stable microbiota plays a crucial role in sustaining various physiological functions, including nutrient metabolism, xenobiotic and drug metabolism, immunomodulation, and antimicrobial defense (Jandhyala et al., 2015). Mounting evidence links ecological destabilization of the gut microbiota to the development of various diseases, including intestinal (Quaglio et al., 2022), hepatic (Chassaing et al., 2014), metabolic (Lin et al., 2020), allergic (Akagawa and Kaneko, 2022), and autoimmune diseases (Yang et al., 2023).

Recent studies propose a potential relationship between the gut microbiota and the development of SP. Patients with NP exhibited higher levels of Bacteroidetes and Proteobacteria and significantly lower levels of Firmicutes compared to healthy controls (Qin, 2022). Similarly, individuals with BP showed a distinct gut microbiota composition, characterized by elevated concentrations of Adlercreutzia, Roseburia, and Uncl. Christensenellaceae (Dekker Nitert et al., 2020). These findings underscore a compelling relationship between gut microbiota and SP. While degenerative spinal diseases traditionally bear the blame for SP, a notable shift toward a younger demographic experiencing SP suggests alternative causative factors beyond structural spinal degeneration (Lei et al., 2015). Consequently, gut microbiota dysbiosis emerges as a significant potential contributor to SP.

In light of these observations, MR offers a promising avenue for exploring causal relationships. MR, first proposed by Smith and Ebrahim (2003), utilizes genetic variation as an instrumental variable, enabling the elimination of confounding bias and reverse causation (Emdin et al., 2017; Soremekun et al., 2022). In this study, we collected data on gut microbiota and SP from the genome-wide association study (GWAS) database, employing MR analysis to discern the causal relationship between them. The study aims to provide innovative insights for the prevention and treatment of SP by unraveling the intricate interplay between gut microbiota dynamics and SP.

To the best of our knowledge, this study stands as the inaugural and thorough investigation employing publicly available GWAS databases to scrutinize the causal relationship between the gut microbiota and four prevalent types of SP—specifically, NP, TSP, LBP, and BP. Through a meticulous analysis of the data, we observed that all IVW results within the dataset for ‘ lumbar and other intervertebral disk disorders with radiculopathy ’ were close to 1, with narrow 95% confidence intervals. This suggests the absence of a significant causal effect between the gut microbiota and this particular type of LBP. Consequently, we opted to exclude the data related to this specific type of LBP. Following a stringent selection process, we successfully identified a total of 37 bacterial genera exhibiting potential causal relationships with SP. Subsequently, through the application of the Benjamini–Hochberg corrected test, we corroborated the strong causal relationship of four bacterial genera with SP. The discoveries emerging from this study serve as an invaluable reference for subsequent research endeavors aimed at preventing and managing SP through precise interventions in the gut microbiota.

The study demonstrates that over 90% of cases involving SP lack a definitive diagnosis related to identifiable causes such as fractures, infections, tumors, etc (Haldeman et al., 2012). Consequently, clinical interventions face challenges in delivering precise and effective targeted treatments, often relying on symptomatic relief measures such as analgesics and soft tissue relaxation (Cheng, 2021). In recent years, growing attention has been directed toward understanding the intricate relationship between the gut microbiota and pain. The gut microbiota, with its array of metabolites, neurotransmitters, by-products, and other mediators, possesses the ability to modulate pain (Guo et al., 2019). In this context, we conducted a comprehensive exploration of the causal relationship between the gut microbiota and SP using Mendelian randomization analysis. Upon subjecting the MR results to the Benjamini–Hochberg corrected test, a strong causal relationship emerged between the gut microbiota and low back pain or/and lower limb pain. However, no significant causal relationship was discerned between the gut microbiota and NP, TSP, or BP. The outcomes of our study align with the observations of Arai et al. (2018), who reported a noteworthy positive relationship between the severity of constipation and the intensity of pain in individuals experiencing low back pain or/and lower limb pain. Notably, the severity of constipation is known to exert a significant influence on the composition of the gut microbiota (Zhu et al., 2014).

We observed that Oxalobacter and Tyzzerella 3 act as risk factors for low back pain or/and lower limb pain, while Ruminococcaceae UCG011 and Olsenella exhibit protective effects. Rajasekaran et al. (2020) identified a higher abundance of Oxalobacter in degenerated intervertebral disks. Intervertebral disk degeneration is widely recognized as a crucial factor in the onset and progression of LBP (Meng et al., 2023). Hence, we posit that Oxalobacter might contribute to LBP by potentially inducing intervertebral disk degeneration. Currently, there is limited clinical or experimental research on Tyzzerella 3 concerning LBP, and direct evidence establishing Tyzzerella 3 as a risk factor is lacking. Some studies found that Tyzzerella can produce aromatic amines and is positively correlated with the occurrence of diabetes (Ruuskanen et al., 2022; Sugiyama et al., 2022). Therefore, Tyzzerella 3 might promote the development of LBP by influencing endocrine or endothelial functions. Regarding the protective bacterial genera identified in the development of LBP, relevant studies on changes in the abundance of Ruminococcaceae UCG011 and Olsenella in the feces of LBP patients or animal models are currently unavailable. Ruminococcaceae UCG011 belongs to the Ruminococcaceae family, and evidence indicates a significant reduction in Ruminococcaceae family bacteria in the feces of mice with lumbar disk herniation compared to the control group (Wang et al., 2021). Butyrate produced by Ruminococcaceae family bacteria can promote the synthesis of vitamin D in the body (Murdaca et al., 2021). Studies have found that vitamin D has a regulatory effect on the immune function of the body, as it can inhibit the differentiation of pro-inflammatory cells such as T helper (Th) 17 cells, thereby reducing the secretion of pro-inflammatory factors such as IL-17 (Murdaca et al., 2011; Yamamoto and Jørgensen, 2020). Therefore, we hypothesize that improving local chronic inflammation in the body may be a potential mechanism for the protective effect of Ruminococcaceae UCG011. Additionally, research indicates that Short-chain fatty acids (SCFAs) produced by Olsenella can mediate the immune balance between Th17 cells and regulatory T cells (Tregs) by activating Tregs’ activity, thus balancing the levels of pro-inflammatory factors (derived from Th17 cells) and anti-inflammatory factors (derived from Treg cells) in the body (Kim, 2021). This could be a potential mechanism by which Olsenella resists the development of LBP. The involvement of the gut microbiota in the development of LBP is an exceedingly complex process. Therefore, the specific mechanisms by which the four identified positive gut microbiota affect low back pain or/and lower limb pain, require further experimental validation in subsequent studies.

In addition to the four bacterial genera strongly associated with SP previously mentioned, our study identified 33 other bacterial genera exhibiting potential causal relationship with SP. To ensure a comprehensive exploration of gut microbiota potentially linked to SP, we incorporated data from all gut microbiota groups with Benjamini–Hochberg corrected test p-values below 0.05. Among the eight bacterial genera potentially causally related to NP, the majority belonged to the Firmicutes phylum. Qin et al. (2019) reported symptom improvement in cervical spondylosis patients following manual therapy, accompanied by a significant increase in the proportions of Lactobacillus and Bifidobacterium in feces, both belonging to the Firmicutes phylum. Unfortunately, limited clinical and foundational research exists on the gut microbiota’s association with NP, and there is no evidence supporting the relationship between Lachnospiraceae UCG010, Escherichia-Shigella, Methanobrevibacter, Eubacterium nodatum group, Faecalibacterium, Subdoligranulum, Butyrivibrio, Ruminococcaceae UCG010, and NP. Potential protective factors for TSP include Butyrivibrio, Ruminococcaceae UCG011, and Eubacterium brachy group. However, similar to NP, research on the gut microbiota and TSP is scarce, lacking supporting evidence. Interestingly, through a comparative analysis of potential causally related bacterial genera in NP and TSP, Butyrivibrio was identified as a shared potential protective genus. Its production of butyrate, propionate, and other SCFAs inhibiting histone deacetylase activity may be one of the potential mechanisms underlying Butyrivibrio’s analgesic effects (Descalzi et al., 2015; Tang et al., 2022). Research on the relationship between gut microbiota and low back pain or/and lower limb pain is more abundant. Yao et al. (2023) found a significant decrease in Lachnospiraceae NK4A136 group, Turicibacter, and Roseburia in the feces of rats in a LBP model compared to the control group. In various LBP animal models, Wang et al. (2021) also found lower abundance of Lachnospiraceae NK4A136 group in rats with lumbar disk herniation compared to the control group. A cross-sectional study revealed a significant reduction in skeletal muscle mass index in patients with LBP compared to normal individuals (Park et al., 2023). Sugimura et al. (2022) found a positive relationship between the abundance of Eisenbergiella and skeletal muscle mass, suggesting a reasonable hypothesis that Eisenbergiella may prevent LBP by increasing lumbar skeletal muscle mass. Consistent with the above findings, our study identified Lachnospiraceae NK4A136 group, Turicibacter, Roseburia, and Eisenbergiella as potential protective factors for LBP. In studies investigating the relationship between BP and gut microbiota, Dekker Nitert et al. (2020) found a higher abundance of the genus Uncl. Christensenellaceae in patients with BP. However, contrary to this conclusion, our results indicate that Christensenellaceae R.7 group is a potential protective factor for BP, a finding supported by Hollister et al. (2020). In summary, this study experimentally validated some of the bacterial genera with potential causal relationships to SP that were screened. This underscores the significance of exploring bacterial genera with potential causal relationships to SP, and the unvalidated genera warrant further investigation.

Whether it is NP, TSP, LBP, or BP, they represent distinct segments of SP. Fundamentally, these pains originate in the spinal column, suggesting a certain degree of interconnectedness among pains occurring in different spinal segments. To dissect this phenomenon, we conducted a comparative analysis of bacterial genera potentially influencing SP across different segments. Our investigation revealed that Ruminococcaceae UCG010 exhibits potential protective properties, common to both NP in the last month and BP in the last month. Similarly, Ruminococcaceae UCG011 emerges as a potential safeguard against TSP, LBP, and the amalgamation of low back pain or/and sciatica. Notably, Butyrivibrio surfaces as a potential protective agent against NP in the last month and TSP. Intriguingly, the Eubacterium nodatum group assumes a potential risk factor role in NP for 3+ months while concurrently acting as a potential protective factor for low back pain or/and sciatica. This nuanced outcome suggests that a singular bacterial genus might exert counteractive regulatory influences on pains manifesting in different spinal segments. In summation, the intricate modulation of pains across different spinal segments by the gut microbiota underscores a complex process. Shared or divergent mechanisms may underscore these phenomena, necessitating further exploration to unveil the underlying intricacies.

Furthermore, to scrutinize potential disparities in causally related bacterial genera associated with SP across varying durations, we incorporated datasets reflecting distinct timeframes— 1 month and 3 months. Regrettably, datasets for different durations of TSP and low back pain or/and lower limb pain, were unavailable. Consequently, our analysis encompassed datasets for 1 month and 3 months of NP and BP. MR outcomes reveal an absence of shared potential causally related bacterial genera between 1 month and 3 months of NP, a trend also mirrored in the context of BP. This suggests a dynamic nature, signifying that bacterial genera with potential causal relationship with SP may evolve during the course of its progression. Contrary to the findings of Dekker Nitert et al. (2020), who observed heightened abundance of Adlercreutzia, Roseburia, and Uncl. Christensenellaceae in patients with 1 month of BP, our MR results challenge this observation. Specifically, Adlercreutzia (P = 0.53) and Roseburia (P = 0.92) do not emerge as potential causally related bacterial genera for 1 month of BP. Instead, the Christensenellaceae R.7 group surfaces as a potential protective bacterial genus for this duration of BP. We posit that discrepancies in results may be attributed to the relatively modest sample size employed in the clinical study. In conclusion, it is imperative to delineate causally related bacterial genera associated with SP at distinct developmental stages. This endeavor holds paramount significance for tailoring precise interventions targeting SP across varying durations.

The robustness of this investigation stems from the application of MR to evaluate the causal relationship between gut microbiota and SP. By leveraging genetic variations as IVs, MR effectively mitigates external confounding factors, thereby bolstering internal validity owing to the inherent randomness and independence of these genetic determinants. Notably, subgroup analyses conducted for distinct durations of spinal pain (i.e., 1 month and 3 months) contribute valuable insights, offering implications for future interventions targeting specific gut microbiota to address SP across varying timeframes. However, our study contends with several limitations. Firstly, the exclusivity of data from European countries prompts the necessity for further experimental validation to ascertain the generalizability of MR results to populations in other regions, such as Asia and Africa. Secondly, the adherence to the conventional significance threshold for SNPs in MR studies (P < 5e−08) restricts the number of selected SNPs, potentially influencing subsequent sensitivity analyses and control for horizontal pleiotropy. Thirdly, the constraint of exposure data to the genus level hampers a more nuanced analysis of the causal relationship between higher taxonomic levels of gut microbiota and SP. Lastly, relying on public databases rather than original sources limits the scope of available datasets, resulting in the omission of subgroup analyses for TSP and low back pain or/and lower limb pain during SP subgroup analyses— a notable constraint in our study.

Through our two-sample Mendelian randomization (MR) analysis, we have successfully identified a comprehensive set of 37 bacterial genera potentially causally related to SP, encompassing NP, TSP, LBP, and BP. Employing the rigorous Benjamini-Hochberg corrected test, we have discerned four bacterial genera that exhibit robust causal relationships with SP. Notably, our analysis has unveiled a potential common regulatory mechanism, suggesting that certain bacterial genera may influence spinal pain across different segments. Furthermore, the dynamic nature of these potential causal relationships has been illuminated, indicating that, as the duration of SP progresses, the involved bacterial genera undergo changes. In conclusion, this study contributes valuable insights into the intricate interplay between the gut microbiota and SP. Such revelations not only serve as a significant reference for understanding these complex connections but also pave the way for future research endeavors aimed at preventing and treating SP through targeted interventions in the gut microbiota.

The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author/s.

SH: Conceptualization, Writing – original draft. LC: Conceptualization, Writing – original draft. XZ: Formal analysis, Writing – review and editing. YH: Data curation, Writing – review and editing. YT: Writing – review and editing. HH: Writing – review and editing. HW: Validation, Writing – review and editing. CY: Validation, Writing – review and editing. ZL: Funding acquisition, Project administration, Writing – review and editing. LL: Funding acquisition, Validation, Writing – review and editing. BY: Writing – review and editing.