Metabolic syndrome (MS) is a multifaceted condition characterized by a cluster of risk factors—including obesity, dyslipidemia, hypertension, and insulin resistance—that significantly elevate the likelihood of developing serious chronic diseases. Emerging evidence highlights a causal link between disruptions in the intestinal microbiome and the onset of MS. Recent advances in microbiome sequencing and multi-omics technologies have deepened our understanding of this connection. In particular, next-generation sequencing (NGS) and the expansion of bioinformatics tools and microbial databases have made it possible to analyze the intestinal microbiota—comprising bacteria, archaea, viruses, fungi, protozoa, and helminths—with unprecedented precision. These technologies provide both genetic and functional insights into microbial communities, laying the groundwork for innovative approaches to diagnosis, prevention, and personalized therapeutic interventions for metabolic syndrome. Metabolic syndrome (MS) refers to a set of conditions that interfere with the body’s metabolism, more precisely in the chemical reactions that occur to regulate homeostasis. This condition is characterized by an increased risk of developing pathologies that include obesity, high blood pressure, hyperglycemia, and dyslipidemia. These are directly related to the host’s genetic susceptibility, environmental factors, and lifestyle (Haffner et al. 1992; Reaven 1988). The criteria used to define an individual with metabolic syndrome, based on the American Heart Association/National Heart, Lung, and Blood Institute (AHA/NHLBI) guidelines, include the presence of three or more of the following risk factors: central obesity, based on ethnicity-specific waist circumference reference, or body mass index >30 kg/m, low HDL cholesterol (men <40 mg/dL and women <50 mg/dL), elevated triglycerides (≥150 mg/dL), high blood pressure (systolic ≥130 mmHg or diastolic ≥85 mmHg), and increased fasting glucose (≥110 mg/dL) (Grundy et al. 2005). In recent years, the prevalence of MS has increased considerably worldwide and is now considered a public health problem that affects all age groups and impacts quality of life. Estimates show that by 2035, the prevalence of MS will increase to 53% (Engin 2017; Sun et al. 2023). This is a problem, given that individuals with MS have a higher risk of developing serious diseases and mortality compared to individuals without MS (Grundy et al. 2005). Several studies have shown that MS is closely related to the gut microbiome. The intestinal microbiome refers to the set of microorganisms, including bacteria, archaea, viruses, fungi, protozoa, and helminths, present in the gastrointestinal tract (Sun et al. 2023; De Jonge et al. 2022; Vijay-Kumar et al. 2010; Sheng et al. 2022). To date, most studies investigating the intestinal microbiome and its relationship with the host are directed at the bacteriome (set of bacteria that make up the gastrointestinal tract). However, studies focused on the virome (set of viruses) and mycobiome (set of fungi) are growing in this field (De Jonge et al. 2022, Nel Van Zyl et al. 2022; Kabwe et al. 2020, Liang et al. 2024). Under normal conditions, the intestinal microbiota is characterized by the predominance of obligate anaerobic members (phyla Firmicutes and Bacteroidetes), bacteriophages or phages (crAss and Microviridae), and yeasts (Shkoporov et al. 2019; Reyes et al. 2010; Auchtung et al. 2018). In contrast, the increased presence of facultative anaerobes (phylum Proteobacteria), phages (Streptococcaceae and Bacteroidaceae), and fungi is indicative of intestinal dysbiosis and the development of MS (De Jonge et al. 2022, Byndloss et al. 2017; Ma et al. 2018). It is important to emphasize that the composition of the microbiome is specific to each individual, which can vary over time due to age, diet, environmental factors, and the anatomical location of the gastrointestinal tract (Rinninella et al. 2019). To investigate the relationship between intestinal microbiota and MS, different techniques are applied to explore the data. At the beginning of the studies, the identification of intestinal microorganisms was performed using culture-dependent techniques, limiting the analyses to cultivable species (Mata et al. 1969; Finegold et al. 1977; Moore and Holdeman 1974). With the advancement of sequencing technologies and the development of large-scale microbiome projects, culture-independent techniques, including the use of amplicon sequencing (16S rRNA gene) and whole genome sequencing (WGS) associated with metagenomic, metatranscriptomic, metaproteomic, and metabolomic approaches, have become the most widely used to explore microbiome data and its relationship in the health and disease process (Eckburg et al. 2005; THE HUMAN MICROBIOME PROJECT CONSORTIUM 2012; Lagier et al. 2012). From the use of these technologies, it was recognized that the composition of microorganisms in the intestine contributes to the regulation of homeostasis. However, the mechanisms that maintain homeostasis have not yet been fully elucidated (Byndloss et al. 2017). Different authors suggest that microbial composition is related to a complex network that includes the immune system, the production of metabolites, and other microbial components (Zeng et al. 2020). Vijay Kumar et al. (2010), showed evidence that obesity is regulated by the immune system. Mice with a genetic deficiency in Toll-like receptor 5 (TLR5) presented changes in the intestinal microbiota and developed features of MS, including hyperlipidemia, hypertension, insulin resistance, and obesity when compared to wild-type mice (control). Furthermore, they observed that the transfer of intestinal microbiota from TLR5-deficient mice to wild-type mice is sufficient to transfer the appearance of MS features in wild-type mice. This indicates that MS may be exacerbated by interactions between the microbiome and the immune system. Another study conducted by Pedersen et al. (2016) demonstrated the association of metabolites derived from branched-chain amino acids (BCAAs) and insulin resistance in humans. Two hundred and seventy-seven individuals without diabetes were investigated. The results showed that the metabolome of individuals with insulin resistance was characterized by increased levels of BCAAs. The intestinal microbiome was enriched for BCAA biosynthesis and deprived of BCAA absorption enzymes. The bacteria Prevotella copri and Bacteroides vulgatus were identified as the main species associated with BCAA biosynthesis and insulin resistance. Furthermore, tests in mice showed that Prevotella copri can induce insulin resistance, aggravate glucose intolerance, and increase circulating levels of BCAAs. In other words, failures in regulation can result in the development of metabolic diseases such as obesity, cardiovascular diseases, and diabetes. These data highlight the importance of advances in techniques for investigating intestinal microbiomes in metabolic syndrome. Furthermore, they reveal the significant potential of these approaches to elucidate the pathogenesis associated with metabolic syndrome and effective interventions through new preventive, diagnostic and therapeutic strategies.