Chronic diseases are now the main global health challenge: according to the World Health Organisation, they account for approximately 74% of deaths worldwide. At the same time, scientific attention has focused on the role of the microbiota – the ecosystem of trillions of microbes that live in our bodies – in health and disease. Recent reviews have highlighted how imbalances in this ecosystem (dysbiosis) can contribute to complex and chronic diseases[2], suggesting that the microbiota itself may be a biomarker and target for new therapeutic strategies. In this context, advanced diagnostic technologies such as multiplex PCR allow these microbial alterations to be measured quickly and accurately, opening up new opportunities for both personalised medicine for chronic conditions and the development of targeted nutraceuticals. Below, we explore the key scientific evidence and why multiplex PCR on the microbiota is emerging as an enabling tool in these fields.

Dysbiosis – pathological alteration of the microbiota – has been associated with numerous chronic diseases. Recent studies have identified specific microbial signatures for different diseases: for example, in patients with inflammatory bowel disease (IBD), there is a systematic decrease in Firmicutes bacteria accompanied by an increase in Proteobacteria and a reduction in Faecalibacterium prausnitzii[3].

In obesity, on the other hand, an increase in the Firmicutes/Bacteroidetes ratio and a decrease in F. prausnitzii have been found, indicating a metabolic imbalance in the gut microbiota[4]. Extraintestinal conditions also show microbial correlations: in individuals with major depression, a deficiency of butyrate-producing bacteria, including F. prausnitzii, has been detected, and this species is considered a promising new-generation probiotic and biomarker[5].

In recurrent Clostridioides difficile infections, dysbiosis is characterised by a drastic reduction in microbial diversity and the absence of key species such as C. scindens, a bacterium that produces protective secondary bile acids[6]. These associations – IBD, obesity, mood disorders, intestinal infections – constitute increasingly robust microbial biomarkers: patterns of bacterial communities whose presence or absence can predict or confirm a pathological state. Early identification of dysbiosis, using targeted multiplex PCR panels or metagenomic techniques, means that the onset of a chronic disease can be anticipated and more timely preventive or therapeutic interventions can be implemented. Butyrate, for example, is a key metabolite produced by commensal Firmicutes: a decrease in its levels in the colon potentially indicates incipient inflammation; measuring it can signal the need for targeted dietary or probiotic interventions. In summary, dysbiosis is not only an interesting condition in the field of research but also a measurable and modifiable factor: knowing the microbial biomarkers linked to chronic diseases provides clinicians with a new set of prognostic indicators and targets on which to act (diet, probiotics, microbiome-based therapies).

To translate knowledge of the microbiota into clinical practice, accessible diagnostic tools are needed. Until now, much of the research on the human microbiome has been based on massive sequencing, which provides a comprehensive picture but requires specialised laboratories, long processing times (days) and high costs. Targeted multiplex qPCR, on the other hand, is a complementary approach geared towards speed and clinical relevance. This technique allows multiple microbial targets of interest – such as specific pathogenic or key commensal bacteria – to be detected simultaneously (in a single test) through the amplification of their DNA. There are many advantages over NGS:

• Response time: A multiplex PCR test can provide results in a few hours, compared to the several days required to sequence and analyse a metagenomic sample. In clinical situations (e.g., assessing dysbiosis in a patient with active colitis), speed is crucial for making rapid treatment decisions.
• Accessibility and cost: qPCR setup is widely available in laboratories, with significantly lower test costs than sequencing. A pre-validated multiplex panel does not require complex bioinformatics: the output is straightforward (presence/absence or quantity of a microbe). This makes it possible to use it even in non-academic centres, clinics or small hospitals, facilitating de facto access to microbiota analysis. 
• Simplified interpretation: qPCR panels are designed to look for specific markers associated with diseases or states of dysbiosis (e.g. low Bifidobacterium spp., an indicator of metabolic dysbiosis). The result is therefore immediately actionable by the clinician, without having to interpret the complex complete microbial ecology.
• Standardisation: while NGS protocols can vary and suffer from bias (e.g. amplification steps, differences in bioinformatics pipelines), multiplex qPCR kits offer standard protocols and calibrated reagents for reproducible diagnostic use, with integrated quality controls.

Of course, NGS remains irreplaceable for comprehensive profiling and discovering new organisms or gene functions; however, for routine clinical use, multiplex qPCR offers a favourable ratio between the information obtained and the effort required. Not surprisingly, a 2023 report by the Association for Molecular Pathology highlights how multiplex panels are rapidly replacing conventional culture and sequencing methods for the diagnosis of infections and microbial imbalances in various areas[7]. This growing adoption is due precisely to the ability of molecular panels to provide targeted answers quickly, improving clinical outcomes through earlier diagnosis and more targeted therapies. From an economic and operational point of view, a well-designed multiplex PCR platform reduces the cost per test and the burden on the laboratory, avoiding the analysis of “excess” data that is not necessary for clinical decision-making. In summary, multiplex qPCR vs NGS is not an either/or choice, but a complementary approach: targeted PCR excels when we know what to look for (known biomarkers of dysbiosis or specific pathogens) and speed is of the essence, while NGS remains the tool for profiling and expanding our knowledge of a patient's microbiota. From a usability perspective, however, multiplex PCR has the characteristics to bring the microbiota into the everyday clinical laboratory, similar to how PCR panels have revolutionised the diagnosis of infectious diseases.

An innovative aspect of preventive medicine is the periodic monitoring of the microbiota in at-risk individuals to identify imbalances even before symptoms or full-blown diseases manifest themselves. Thanks to multiplex PCR kits targeting different areas, it is now possible to envisage microbiota screening programmes in the following areas:

• Intestinal: evaluate the composition of the intestinal flora in individuals with a family history of inflammatory or metabolic diseases, in order to detect early signs (e.g. a decrease in butyrate-producing bacteria, or an abnormal increase in pro-inflammatory Proteobacteria). This could guide interventions on diet, pre/probiotics or other measures to prevent the development of disease.
• Vaginal: a balanced vaginal microbiota is known for its dominance of Lactobacillus spp., which maintain a protective acidic pH. Regular microbiological screening in women with a history of vaginosis, candidiasis or obstetric complications can detect vaginal dysbiosis (e.g. decrease in lactobacilli, increase in Gardnerella and anaerobes) and allow for timely treatment. Studies show that a healthy vaginal microbiota offers colonisation resistance to pathogens and positively modulates the local immune response[8].
• Skin: the skin hosts a diverse microbiota that acts as a first line of defence. In individuals predisposed to dermatitis, chronic wounds or recurrent skin infections, periodic analysis of the skin flora (e.g. testing for pathogenic Staphylococcus aureus or reduced presence of beneficial commensals such as Staphylococcus epidermidis) can indicate a state of risk. For example, S. epidermidis produces molecules that attenuate skin inflammation and stimulate protective antimicrobial peptides[9]; its deficiency could suggest a weakened skin barrier. Intervention with topical probiotics or other therapies could prevent flare-ups.

These multi-district profiles make the concept of predictive medicine feasible: instead of waiting for a chronic disease to appear, modifiable microbiological indicators are monitored. Multiplex PCR is particularly suitable for this purpose, as it is minimally invasive (a stool sample, vaginal or skin swab is sufficient), repeatable over time and relatively inexpensive. In the future, we could include microbiota analysis in routine check-ups: for example, an “intestinal microbiota panel” for the over-50s focused on markers of inflammation and metabolism, or a “vaginal microbiota panel” for pregnant women to prevent preterm births linked to vaginosis. The data obtained will enrich traditional clinical assessment with a personalised biological dimension, enabling prevention plans tailored to individual microbial profiles. Last but not least, this practice will raise awareness of the importance of lifestyles that maintain a healthy microbiota (a fibre-rich diet, avoiding unnecessary antibiotics, etc.), actively involving patients in protecting their own health.

The possibility of targeted measurement of components of the microbiota is already finding concrete applications in various medical specialities, contributing to a more personalised approach to chronic diseases:

Gastroenterology

This is perhaps the most advanced area. In patients with IBD, multiplex PCR panels allow the quantification of key bacterial populations related to disease progression (e.g. Faecalibacterium prausnitzii, whose abundance is inversely correlated with inflammation). These tests can be used to monitor remission or predict relapses, alongside traditional inflammatory markers. In irritable bowel syndrome (IBS), microbial signatures are being evaluated to better sub-type patients (fermentative dysmetabolism vs. subclinical inflammation) and tailor diet and therapy accordingly. In obesity and metabolic syndrome, as already mentioned, the gut microbial profile (e.g., F/B ratio, presence of Akkermansia muciniphila) can provide information on the patient's metabolic and inflammatory status and on the expected response to dietary interventions[4]. A 2024 review emphasises that the gut microbiota is a crucial factor in the host's energy homeostasis and directly influences phenomena such as fat accumulation, metabolic inflammation and even appetite modulation[4]. This opens up the prospect of using targeted interventions on the microbiota (diet, specific pre/probiotics) as adjuvants in the management of obesity and metabolic diseases, measuring their effectiveness with serial qPCR tests.

Immunology

The link between microbiota and the immune system is profound – just consider that a large part of the immune tissue resides in the gut (GALT). Some commensal bacteria produce molecules with immunomodulatory effects: Bacteroides fragilis, for example, synthesises polysaccharide A, which stimulates the maturation of regulatory T cells and the production of IL-10, helping to contain inflammation[10]. Multiplex panels designed to detect specific “immunomodulators” in the microbiota make it possible to assess the ability of a microbiota to support immune tolerance. In models of colitis, the absence of certain commensals is associated with more severe inflammation, while their reintroduction (via new-generation probiotics) can alleviate the disease. This idea is the basis for so-called “next-generation probiotics”: strains selected for specific beneficial functions. For example, prototypical strains of B. fragilis are in advanced stages of study as an experimental therapy to rebalance the intestinal immune system. Multiplex PCR acts both as a companion diagnostic (confirming the presence/absence of the beneficial strain after administration, or measuring its impact on secondary markers) and as a tool for stratifying patients eligible for such therapies (identifying those with a specific microbial deficiency). Microbiota is also being studied in the fields of allergy and autoimmunity: one example is type 1 diabetes, where intestinal dysbiotic patterns in children are correlated with the subsequent development of the disease – knowledge that could lead to immunopreventive interventions.

Neuroinflammation (Gut-brain axis)

Discoveries about the bidirectional link between microbiota and the nervous system are revolutionising concepts in neurology and psychiatry. The case of depression is emblematic: a large-scale study has highlighted a reduction in intestinal butyrate producers (such as Faecalibacterium) in individuals with depressive symptoms, suggesting a link between low-grade inflammation, microbial metabolites and brain neurochemistry [5]. This has given rise to innovative approaches such as psychobiotics – probiotics or microbial consortia designed to modulate mood through the gut-brain axis. A multiplex PCR test could, for example, assess the presence of bacteria capable of producing GABA, serotonin or other peripheral neurotransmitters to identify imbalances associated with anxiety or mood disorders. In the field of neurology, pioneering studies show that the microbiota can influence the course of neurodegenerative diseases. This indicates that certain microbial signals contribute to the pathogenic process. In the future, qPCR panels could be used to detect pro-inflammatory microbial metabolites (e.g., excess of specific bacterial products such as LPS, tryptophan metabolites) in neurological patients or to monitor the impact of additional dietary/probiotic interventions in controlling neuroinflammation. The field of anti-ageing and regenerative medicine is also looking at the microbiota: centenarians, for example, have unique gut microbiota profiles associated with lower inflammation and favourable metabolites (short-chain fatty acids, specific bile acids). The idea is that modulating the microbiota could mitigate inflammaging (the chronic inflammatory state of the elderly) and promote healthier ageing. Specialised multiplex kits could in future become part of geriatric assessment, identifying elderly people with “fragile” microbiota who need intervention.

Precision oncology

Finally, a mention of the emerging connection between microbiota and cancer therapy. It is known that the composition of the gut microbiota can influence the response to immunotherapy drugs (checkpoint inhibitors) in patients with solid tumours. Biotech start-ups are developing PCR panels to profile faecal bacteria before starting certain immunotherapies, in order to predict who will respond better or worse (and potentially modulate the microbiota to improve response). Similarly, in some gastrointestinal tumours (e.g. colorectal cancer), the microbiota is being investigated for the presence of pro-inflammatory pathobionts (such as Fusobacterium nucleatum) that could constitute prognostic biomarkers and targets for complementary interventions. Although these uses are still in the experimental phase, they clearly illustrate the versatility and power of the concept: measuring the microbiota to personalise medicine.

The combination of microbiota diagnostics and the nutraceutical industry is generating new opportunities for innovation. Traditionally, nutraceutical products (probiotics, prebiotics, functional supplements) are developed and marketed with generic wellness claims. Now, thanks to the availability of simple and rapid microbiota tests, it is possible to adopt a much more evidence-based and personalised approach:

• OEM co-development: imagine a nutraceutical company (OEM) that wants to launch a new supplement for gut health. In partnership with a multiplex diagnostic platform, it can design an integrated product+test package from the outset. For example, a supplement containing prebiotic fibres and probiotic strains is developed alongside a specific multiplex PCR kit to measure the effect on the user's microbiota (increase in Bifidobacterium and Lactobacillus, butyrate production, etc.). The test becomes a companion diagnostic provided to the customer or healthcare professional: before supplementation, a baseline of the microbiota is obtained, then after a few months of intake, the change is objectively verified. This model not only provides real-world efficacy data (also valuable for the company to improve the product), but also increases the perceived value of the nutraceutical in the eyes of doctors and consumers, differentiating it in the market. Ulisse Biomed, with its technological platform, can support the OEM in all phases: from the selection of the most relevant microbiological targets for the health claim, to the development of the dedicated multiplex panel, to cloud data management for post-marketing studies.
• Advanced personalisation (‘digital nutraceuticals’): diagnostic integration paves the way for personalised nutraceutical services. For example, a functional medicine centre could offer patients a programme in which, based on an initial microbiota test, a tailor-made probiotic or supplement is formulated (choosing strains and ingredients targeted at correcting the imbalances identified). After a few weeks, a new test checks progress and the formulation can be adjusted. This creates a virtuous cycle of testing and tailoring, closely resembling the precision medicine approach in the pharmaceutical field. Multiplex tools make this process feasible in a short time and at a sustainable cost. Consider the case of a personalised diet: instead of generically recommending “more fibre for everyone”, a molecular nutritionist could test the patient's microbiota and discover, for example, a deficiency of propionate producers; then formulate a diet/supplement rich in inulin to selectively feed those populations, and finally measure the actual increase in Bacteroides (the main propionate producers) with PCR. This level of precision transforms nutraceuticals from generic products to measurable interventions, gaining scientific credibility. 
• Companion diagnostics for advanced probiotics: Probiotics indicated for specific conditions (e.g., Bifidobacterium longum for mild anxiety, pasteurised Akkermansia muciniphila for metabolic syndrome) are beginning to appear on the market. Doctors may be hesitant to recommend them until they have tools to understand who really needs them. This is where a companion microbiota test comes in: to check whether that patient actually has the deficiency or imbalance that the probiotic aims to correct. For example, a test could quantify A. muciniphila in the stool of an obese patient: if it is very low, the doctor has an objective rationale for recommending the Akkermansia supplement. After a few months, a follow-up test confirms the actual colonisation/improvement of the metabolic marker (e.g., reduction in circulating LPS endotoxin, related to the increase in Akkermansia). This model of “nutraceutical companion diagnostics” elevates the role of the microbiota as a biomarker for non-pharmacological therapies and aligns the supplement sector with evidence standards typical of the pharmaceutical industry.
• R&D and nutraceutical clinical trials: finally, the use of multiplex panels is invaluable in the research and development of new nutraceuticals. It allows agile pilot studies to be carried out by objectively measuring the impact of formulations on the microbiota: for example, an 8-week trial of supplement X can easily monitor the increase or decrease of 20 target bacterial strains in participants, obtaining robust quantitative data. This speeds up the product optimisation phase. Similarly, in scientific publications supporting nutraceuticals, the inclusion of microbiological data (obtained via qPCR) adds weight to the conclusions. Collaboration between nutraceutical companies and diagnostic centres such as Ulisse Biomed can therefore result in better, validated products with a more robust regulatory pathway. In a crowded market, being able to say that “our supplement has been tested with molecular diagnostics showing a 50% increase in beneficial XYZ bacteria” is a huge competitive advantage.

In summary, the convergence between microbiota diagnostics and nutraceuticals inaugurates a new paradigm: that of integrated solutions, in which data guides choices and each individual can find the intervention best suited to their biological profile. Ulisse Biomed, with its expertise in both multiplex PCR and cloud data management, is ideally positioned to facilitate this leap forward, offering OEM and clinical partners not only kits, but an entire ecosystem to bring truly evidence-based nutraceuticals to market.

A key factor in spreading the use of multiplex PCR for microbiota is the availability of portable, user-friendly platforms that allow testing to be carried out wherever it is needed, from small hospital laboratories to local clinics. This is where Hyris System™ comes in, the molecular platform developed and used by Ulisse Biomed, consisting of miniaturised bCUBE™ thermocyclers, bAPP™ cloud software and a line of stabilised reagents. The technological heart, bCUBE™, is a PCR device the size of a book, but with central laboratory performance: it performs multiplex qPCR cycles with high sensitivity and specificity, and is designed to be connected (IoT) and managed remotely via the cloud application. This means that a network of bCUBE devices in various clinics or centres can be monitored centrally, with data flowing into the cloud for advanced analysis (e.g. application of AI algorithms for pattern recognition). For microbiota diagnostics in chronic diseases, Hyris System™ offers several operational advantages:

• Decentralisation: functional clinics and specialist centres can perform microbiota testing in-house without having to send samples to distant laboratories. For example, a functional gastroenterology practice can equip itself with a bCUBE™ and obtain the patient's intestinal dysbiosis profile in 1–2 hours, during the same visit. This drastically reduces reporting times and allows the results to be discussed with the patient immediately, improving adherence and understanding.
• Ambient-stable reagents: An innovative feature is the room-temperature-stable, lyophilised reagent kits developed by Ulisse Biomed. This eliminates the need for a cold chain and simplifies logistics: multiplex PCR panels (e.g., the Intestinal Microbiota Core Panel) can be shipped and stored in clinics without refrigerators, ready for use. For decentralised facilities with limited resources, this means being able to offer high-quality molecular testing without additional investment in laboratory infrastructure.
• Ease of use and automation: Hyris System™ is designed for users who are not experts in molecular biology. The operator only needs to add the prepared sample to the reagent cartridge, insert it into the device and start the test via a tablet/computer. Data analysis is automated by bAPP™: at the end of the run, the system provides a clear report with a list of detected/undetected targets and relative quantifications, possibly supplemented with customised interpretations (e.g., “Reduced presence of F. prausnitzii: possible indicator of intestinal inflammation”). This integrated ‘sample-to-answer’ approach makes the technology usable even in the absence of a dedicated molecular biologist, a key feature for penetrating private clinics and non-academic centres.  
• Scalability and cloud integration: each bCUBE™ functions as an independent module; a clinic can start with one device and add more as test volume grows. Thanks to cloud management, multiple devices can be coordinated and monitored remotely, implementing a true distributed diagnostics model. For example, a regional reference laboratory could monitor the quality of tests performed by bCUBE devices in various clinics across the region, or collect all anonymous data to build an epidemiological database of the microbiota. This network vision also allows for microbial surveillance programmes for chronic conditions: for example, tracking the evolution of dysbiosis profiles in a population of diabetic patients undergoing a certain intervention, identifying common trends and correlations with clinical outcomes.
• Panel versatility: the Hyris platform can host different multiplex panels. In addition to the core intestinal panel, there are specific panels for vaginal, oral and skin microbiota, which can even be customised for particular research projects. All these tests can run on the same bCUBE with simple kit changes, maximising return on investment.

In a scenario where local medicine and telemedicine are becoming increasingly important, solutions such as Hyris System™ bring sophisticated molecular testing closer to the patient. An apt comparison can be made with the revolution in rapid COVID diagnostics: from swabs processed only in central laboratories to widespread point-of-care devices. Now the same philosophy can be applied to the diagnosis of chronic diseases through microbiota. This can have a profound impact, especially for patients with reduced mobility or in remote areas: instead of having to travel for specialist microbiota tests, they can have them done at their local centre, perhaps with an operator collecting the sample at home and analysing it with bCUBE on site.

Chronic disease medicine is entering a new era in which the microbiota ecosystem is becoming an integral part of every patient's clinical picture. Having tools to analyse this “invisible organ” means being able to tackle complex diseases from a new and more personalised angle. Multiplex PCR applied to the microbiota is emerging as a key enabler: combining scientific rigour (objective molecular evidence) and practicality (speed and widespread availability), it allows knowledge about the microbiome to be transformed into concrete actions. From the cases discussed, it is clear that in many areas – from monitoring IBD or diabetes to preventing recurrent vaginosis and providing tailored nutraceutical support – the ability to measure microbes offers a strategic advantage. Microbiota is no longer just a scientific curiosity: it has become a clinical parameter to be assessed and optimised, just like blood pressure, blood sugar or lipid profile.

In this scenario, Ulisse Biomed positions itself as an ideal technology partner. Thanks to the Hyris System™ platform and the rapid qPCR panels developed, the company offers clinics and industrial partners a powerful tool for measuring, monitoring and modulating the microbiota in a clinically relevant way. The company is already investing in the creation of a vertical entirely dedicated to the microbiota, integrating advanced diagnostics, predictive algorithms (AI) and customised OEM solutions. This means that in the near future we will see increasingly targeted kits (perhaps specific for lung microbiota or metabolic dysbiosis subtypes), protocols optimised for specific areas (intestine, vagina, skin) and even subscription services for continuous microbial monitoring of chronic patients. The vision is to transform Ulisse Biomed's technological know-how into application leadership: bringing what was previously confined to research laboratories into everyday clinical workflows.

In conclusion, the analysis of microbiota using multiplex PCR represents a fundamental step towards developing more accurate, predictive and personalised chronic medicine. From early diagnosis to targeted therapy, through prevention and the development of effective nutraceuticals, this integrated approach promises benefits for all stakeholders: patients with tailored treatments, doctors with new decision-making tools, and companies with truly effective products. Ulisse Biomed, with its expertise and technologies, already has the tools – and the vision – to lead this change, establishing itself as a partner of choice for both clinical settings and the nutraceutical industry seeking evidence-based solutions. Once revealed and measured, the microbiota ecosystem becomes a foundation on which to build innovation and long-term health.