Systemic Lupus Erythematosus (SLE) is a chronic, autoimmune, multisystem inflammatory disease. Given its complex multifactorial nature, its pathogenesis is not yet fully understood, assuming both genetic and environmental predisposing factors (Tsokos et al., 2016). The complexity of its differential diagnosis lies in its clinical heterogeneity. It mainly affects the kidneys, lungs, skin, joints, blood components and the central nervous system. SLE is one of the most prevalent autoimmune diseases, characterized by a cyclical course, where periods of exacerbations and remissions alternate. The prevalence of SLE varies between 20 and 150 cases per 100,000 people, the numbers seem to be increasing as its identification becomes easier and survival rates improve (Tsokos, 2020). SLE is distributed worldwide, affecting both sexes; however, its prevalence and severity differ depending on the geographic region, as well as the ethnicity of the patients, with a higher proportion observed in populations of black, Hispanic, and Asian ethnicity (Pons-Estel et al., 2017), being more common in urban areas than in rural areas (Gergianaki et al., 2019). The highest rates are found in non-Caucasian adult women (Rees et al., 2017).

Currently differential diagnosis for SLE is determined by clinical manifestations and laboratory test results. The recently introduced classification criteria by the European and American Rheumatology Associations (EULAR/ACR, 2019) relies on positive antinuclear antibodies or ANAs, also known as antinuclear factor (ANF) as the initial requirement. These criteria assign different weights to specific factors, ranging from a score of 2 (for symptoms like delirium, non-infectious fever, and antiphospholipid antibodies (APS) to a score of 10 (for the presence of class III or IV lupus nephritis). These criteria organize items into domains, where only the highest-scoring item within each domain is considered. Instead of numerous specific exclusions, a singular rule applies universally: attributing items to SLE and counting them only when no other diagnosis appears more probable (EULAR, 2019). Even though these criteria exist, patients do not always have all the clinical or biochemical features required to confirm the diagnosis. Therefore, it is of great importance to find integral algorithms that can interpret the patient's clinical situation at the time of debut, as well as the degree of disease progression to provide appropriate treatment.

In recent years, the field of immunology has been revolutionized by the growing understanding of the fundamental role of the intestinal microbiota in the induction, training, and function of the host immune system. In return, the immune system has largely evolved as a means of maintaining the host's symbiotic relationship with these highly diverse and changing microbes. Under favorable conditions, the alliance between the immune system and the commensal microbiota allows the induction of protective responses against pathogens and the maintenance of regulatory pathways involved in maintaining tolerance to harmless antigens. However, profound changes in the environmental context could lead to the selection of a microbiota that lacks the resilience and diversity necessary to establish balanced immune responses (Zhang et al., 2021). Recent studies demonstrate that intestinal dysbiosis in patients with SLE would have a direct effect on the phenotype and functions of T cells, B cells and plasmacytoid dendritic cells (pDC), promoting the disruption of immunological tolerance to self-reactive T or B cell clones in the gut (Tsokos, 2011, Chen et al., 2021). In this sense, there is an increasing number of works that correlate autoimmune antibodies with dysbiosis phenomena in SLE, placing the microbiome as a key actor in its pathogenesis (Chang and Choi, 2023) (Monticolo et al., 2023).

Likewise, considering microbiomes as dynamic ecosystems of hundreds to thousands of members communicating with each other, studying the dynamics of expression of non-coding RNAs (ncRNAs) in different biological environments of patients with LES, proposes defining personalized diagnostic strategies, as well as bringing light to microbiota-host interaction mechanisms in an inter-kingdom context (Chi et al., 2021, So et al., 2021). The use of ncRNAs as biomarkers of complex pathologies with an inflammatory component is a field of study in an exponential phase of exploration. miRNAs are the most widely studied family of ncRNAs given their well-known mechanism of regulation of gene expression and the massive public data currently available. Furthermore, as they regulate specific biological processes, their phenotypic correlation is useful for understanding the molecular pathophysiology of diseases of unknown etiology such as SLE. There is growing evidence that certain miRNAs act as negative regulators of protein expression, closely related to the pathogenesis of SLE, which makes them potential biomarkers to discriminate phenotypes associated with the pathology (Chen et al., 2021, Tan et al., 2021). It has been shown that hsa-miR 146a, hsa-miR-155–5p, hsa-miR-21, hsa-miR-181a and hsa-miR-196a present a positive correlation at the systemic level in patients with SLE (Zhang et al., 2019). However, studies that point to the intestinal expression of these miRNAs are almost null, which makes it challenging to elucidate their role not only in pathogenesis and progression, but also in the transkingdom communication in dysbiosis contexts (ANON, 2018). In particular in this work, we selected 3 miRNAs previously associated with SLE at systemic level: hsa-miR-146a-5p, hsa-miR-155–5p and hsa-miR-223–3p, to evaluate their fecal expression in SLE, and discuss their possible potential role as biomarkers. These specific miRNAs have been systematically studied in the context of different complex diseases, as they are responsible for the regulation of the expression of toll-like receptor 4 (TLR4), which is known to be a key player in the inflammatory response in different autoimmune disorders (Chi et al., 2021, Penas-Steinhardt et al., 2012, Rosso et al., 2022, Dong et al., 2019, Abdul-Maksoud et al., 2021)

Overall, it is worth noting that in Argentina, there is a lack of solid and representative epidemiological studies to explore the modifiable risk factors and phenotypes of SLE in this region (Barber et al., 2021). Considering that the South American continent is home to more than 400 million people, it is expected to represent a significant proportion of those affected by SLE in the world. This translates into a notable diagnostic challenge, especially in underdeveloped countries where access to diagnosis or treatment is not always guaranteed for chronic diseases. In the present work, gut microbiota and the presence of specific fecal miRNAs were analyzed in SLE and non-SLE individuals. This data was integrated with clinical and biochemical markers considered important in the follow-up of patients with SLE, with the aim of generating integral diagnostic tools to discriminate phenotypes. Moreover, we provide new insights into data analysis algorithms to promote innovative phenotyping tools through quantitative and qualitative analysis in a transkingdom interaction network context.