Systemic lupus erythematosus (SLE) has a wide spectrum of clinical and immunological manifestations as an autoimmune disease. Lupus Nephritis (LN) stands out as a prevalent and serious condition with high degree lethality for individuals with SLE. LN haunts a substantial percentage of adults (30-60%) and the majority of children (70%) diagnosed with SLE (Yu et al., 2017; Davidson et al., 2019; Catalina et al., 2020). The varied and unpredictable nature of disease manifestations and fluctuations in disease activity pose significant challenges in accurately diagnosing and effectively managing SLE (Gasparotto et al., 2020). Certainly, the complexity and variability of SLE symptoms suggest that the disease is not a single phenotype, but rather a highly complex and diverse entity (Azzouz et al., 2019). The current diagnosis of SLE primarily depends on clinical manifestations and laboratory tests, including antinuclear antibodies (ANA), anti-double-stranded DNA (anti-dsDNA), and anti-Smith antigen (anti-Sm). However, the sensitivity and specificity of these markers are relatively low. Despite the fact that LN patient’s prognosis have ameliorated over the prior three decades, its treatment remains challenging, and require a comprehensive understanding of the underlying pathogenesis (Anders et al., 2020). Therefore, it is essential for SLE patients to monitor their kidney function and seek appropriate medical care if LN is suspected or diagnosed. The benchmark procedure for detecting LN is renal biopsy (Mejia-Vilet et al., 2022); but the approach is invasive and carry the risk of excessive bleeding that may cause the death of patients (Yang et al., 2021). Additionally, kidney biopsies are not convenient for rheumatologists to continuously monitor disease progression in patients. Hence, novel noninvasive biomarkers for SLE diagnosis, monitoring, and prognosis were urgently needed.

The subject of majority of investigations of SLE has been focused on the gut microbiota while urinary microbiome is rarely explored (Ling et al., 2017; Lundy et al., 2021; Miller et al., 2022). Recent investigations have weakened the customary notion that claims urine is sterile by indicating the presence of varied microbial systems in the urinary system (Ainsworth, 2017). In fact, this community of microorganisms has influence on health of urinary tract and could contribute to the onset and course of certain urological ailments. Updated research has indicated the potential involvement of urinary microbiome both in the etiology of urinary tract infections as well as in the preservation of urinary tract wellness, bladder cancer, and other urinary disorders (Bucevic Popovic et al., 2018; Martin et al., 2022). Additionally, the urinary microbiome has been linked to other physiological processes such as immune function (Liu et al., 2017) and neurological function, highlighting the far-reaching impact of this microbial community on overall health. Therefore, studying the urinary microbiome holds great potential for developing novel diagnostic and therapeutic approaches for a variety of urological conditions. Hai Bi et al. identified that urinary microbiota may serve as a potential biomarker and therapeutic target for bladder cancer (Bi et al., 2019). Jiayang Jin et al. demonstrated that the urinary tract microbiota profile in rheumatoid arthritis (RA) is characterized by increased microbial richness and altered taxonomic composition, which correlates with the disease’s immunological and metabolic changes, highlighting the interaction between urinary microbiota and host autoimmunity (Jin et al., 2023). However, little is known about their function in autoimmune illnesses, specifically in SLE.

In this study, urine specimens samples were analyzed using 16S rRNA gene sequencing to gain detailed insights into the urinary microbiome. The findings suggest a potential role of urinary microbiome dysbiosis in the pathogenesis of SLE.

SLE is an autoimmune disease characterized by the involvement of one or more organs, including the skin, kidneys, joints, and nervous system, and take a chronic or relapsing and remitting disease course (Zimlichman et al., 2014; Durcan et al., 2019; Parikh et al., 2020; Tsokos, 2020; Lou et al., 2022). There are six distinct histological groups of LN that are distinguished from one another by the severity of their involvement with the kidneys in LN and their specific symptoms and varied treatment approaches (Anders et al., 2020). Over the past few decades, immunosuppressive medication, commonly with mycophenolate mofetil or cyclophosphamide and glucocorticoids, is the conventional course of action for LN. Despite advancements in treatment and diagnostic option, LN is still considered the most lethal for SLE patients (Morales et al., 2021). The numerous comorbidities linked to immunosuppressive therapy, such as infections, osteoporosis, cardiovascular consequences, and reproductive issues, are alarming (Aziz and Chaudhary, 2018; Yu et al., 2022). Rapid and precise LN diagnosis and prompt start of treatment can be vitally beneficial for improving the ultimate outcomes in SLE patients. In this work, urine microbiomes of three groups (HCs, SLE with LN and SLE without LN) were performed by16S rRNA sequencing. We have further developed a diagnostic model consisting of a panel of different bacterial in identifying LN from SLE patients. This research provides a new avenue of research focusing on the changes of urinary microbiome in SLE patients and establish connections between specific urinary genera and clinical parameters.

Infections are considered important environmental triggers of autoimmunity and can contribute to autoimmune disease onset and severity (Qiu et al., 2019). Mirei Shirakashi et al. found that defective T cell receptor (TCR) signaling alters the gut microbiome and promotes systemic autoimmunity by driving the differentiation of Th17 cells (Shirakashi et al., 2022). Seung-Chul Choi et al. discovered that gut microbiota dysbiosis and altered tryptophan catabolism contribute to autoimmunity in lupus-susceptible mice (Choi et al., 2020). However, the etiologic mechanism between urinary microbiota and the occurrence of LN in SLE patients remains not fully understood. There is emerging proof that the pathophysiology of numerous autoimmune illnesses is influenced by abnormalities in the gut microbial flora (Rosser and Mauri, 2016) including type 1 diabetes (Gulden et al., 2018), rheumatoid arthritis (Zhang et al., 2015), multiple sclerosis (Cignarella et al., 2018), inflammatory bowel disease (Schirmer et al., 2019) and SLE (Silverman, 2019; Tomofuji et al., 2021; Chen et al., 2022). It is found that Ruminococcus gnavus (RG) intestinal expansions and overall disease activity has direct correlation primarily in LN patients (Azzouz et al., 2019). However, there is limited research investigating the association between renal and urinary microbiota involvement in SLE. Pachucki RJ et al. find that persistent bacteriuria and antibodies recognizing curli/edna complexes from Escherichia coli are linked to flares in systemic lupus erythematosus (Pachucki et al., 2020). For many years, a urologist’s concern with urine bacteria culture was limited to making a diagnosis of a urinary tract infection. However, a research investigation involving 77 catheterized patients revealed the presence of 78 unique bacterial species in their urinary tracts, thus challenging the previously held notion of sterility within the urinary tract (Thomas-White et al., 2018). Besides, our research (Yang et al., 2022) and others (Nejman et al., 2020; Narunsky-Haziza et al., 2022) have also revealed that the bacteria and fungi within tumors were located in both immune and malignant cells and that the composition varied according to tumor type and this awareness could also be extended to the bladder.

Thus, this work showed that SLE patients with LN and without LN exhibited significant variations in the bacterial profiles of their urine compared to the HC group. In comparison to the SLE group, notable disparities were observed in the α diversity of bacterial markers specifically within SLE patients with LN, as evidenced by variations in the Shannon and Simpson indices. These important findings offer insights into how the microbiome of urinary system may be involved in the SLE progression. It also lay the foundation for further research on understanding the mechanisms behind urinary microbiota dysbiosis in SLE patients. Streptococcus and Prevotella showed decreased abundance in SLE patients with and without LN than its abundance in HCs. Notably, Gardnerella which is commonly associated with vaginitis has high abundance in the urine bacteria of SLE patients which consistent with the previously reported trend of the gut microbiota and to be proved negatively correlated to the Lactobacillus abundance in their vagina (Ling et al., 2023). These results imply potential interactions between that vaginal and urinary microbiota. Research efforts directed at exploring the connections between these two microbiomes can be of high value. Of particular interest, our study reveals that Sphingomonas, Lachnospiraceae are positively correlated with vitamin D, cylinderuria, and proteinuria while Pedobacter, Aquabacterium, Delftia, Achromobacter displayed a negative correlation with proteinuria and ACR. Vitamin D receptor ligands can mediate immunosuppressive effects. Studies have reported that vitamin D may play a regulatory role in the interferon alpha amplification loop in SLE (Ben-Zvi et al., 2010). Therefore, we propose that the microbiome may mediate vitamin D receptor regulation of interferon alpha, contributing to the exacerbation of SLE. Moreover, administration of Lactobacillus spp. to mice with LNs can influence its progression by enhancing immune regulation, providing protection against vascular diseases, or exerting anti-inflammatory effects. Therefore, Lactobacillus appearance in urine of LN patients may potentially highlight a protective effect. In addition, functional prediction of unique bacteria using Picrust2 and KEGG analysis showed that these unique bacteria may regulate protein families involved in signaling and cellular processes, vitamins and cofactors metabolism, indicated to influence the SLE progression.

The dysbiosis within the gut (Zheng et al., 2023), subgingival (Correa et al., 2017), cutaneous (Huang et al., 2020), oral (van der Meulen et al., 2019) and vaginal (Ling et al., 2023) microbiomes of SLE patients have been implicated in contributing to immune dysregulation. For the first time, we observed a correlation between urinary microbiota and disease immune markers in SLE patients. However, we must acknowledge the limited size of our single-center urine samples and the large percentage of unidentified taxa are two factors that restrict our existing data. Additionally, further exploration of how microbiota-modulating therapies, such as probiotics and antibiotics, may influence disease progression in SLE patients is a valuable direction for future research. Also, diagnostic markers in the urine samples for LN, using only bacterial genera, which is a big limitation for the data. To address these limitations in future studies, we will recommend implementing longitudinal designs to track changes over time and employing metagenomic analyses to capture the complexity of the microbiome. These approaches could significantly enhance the validity of our findings and provide deeper insights into the interactions between microbial communities and SLE. Lastly, we did not conduct functional validation and mechanistic studies to exclude potential influences from fungi or viruses among the differing microbial taxa, which necessitates further investigation in future research. In summary, our research is the first to indicate the potential use of urinary bacterial markers for predicting LN by outlining the variation in urine mycobiome equilibrium between the groups with and without LN in SLE.