Microbiome Concordance Index Score:

A Comprehensive Framework for Systemic Disease Correlation

The Microbiome Concordance Index Score, developed by Dr. Eduardo Beltran, in 2019, is an innovative diagnostic and prognostic tool designed to evaluate the interplay between gut microbiome imbalances, systemic inflammation, and their contributions to a broad spectrum of diseases, including autoimmune conditions, metabolic syndrome, and cancer. This multiparametric system synthesizes findings from the GI MAP, SIBO breath test, intestinal health markers, and clinical symptoms into a unified scoring model to assess microbiome dysfunction comprehensively.

Unlike tools that focus solely on SIBO (Small Intestinal Bacterial Overgrowth), this scoring system recognizes that dysbiosis can occur in many forms, including:

• LIBO: Large Intestinal Bacterial Overgrowth

• LIFO: Large Intestinal Fungal Overgrowth

• LIMO: Large Intestinal Methanogen Overgrowth

• SIBO: Small Intestinal Bacterial Overgrowth

• SIFO: Small Intestinal Fungal Overgrowth

• IMO: Intestinal Methanogen Overgrowth

Patients with a negative SIBO breath test may still experience significant microbiome-related dysfunction, as dysbiosis in other regions of the gastrointestinal tract can drive systemic disease processes. The Microbiome Concordance Index Score provides a comprehensive framework to evaluate these cases, even when SIBO-specific diagnostics are inconclusive.

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GI MAP and Breath Test Correlation (Maximum: 30 points)

This category evaluates the correlation between bacterial or fungal species identified in the GI MAP and gas production (hydrogen, methane, and hydrogen sulfide) measured during the SIBO breath test. The scoring recognizes that microbial overgrowth and their metabolites may occur beyond the small intestine, affecting overall gut and systemic health.

Scoring Parameters

• Gas Profiles: Hydrogen, methane, and hydrogen sulfide are each evaluated, contributing up to 10 points per gas type. A negative SIBO breath test does not preclude scoring in this category, as dysbiosis in other regions (LIBO, LIFO, etc.) can still align with microbial imbalances identified in the GI MAP.

• Species-Specific Correlations:

  • Hydrogen-Producing Bacteria (Escherichia coli, Klebsiella spp., Enterococcus spp.): Linked to diarrhea, gut inflammation, and metabolic endotoxemia.

  • Methane-Producing Microorganisms (Methanobrevibacter smithii, Methanosphaera spp.): Associated with constipation, metabolic syndrome, and colonic overgrowth (LIMO).

  • Hydrogen Sulfide-Producing Bacteria (Desulfovibrio spp., Bilophila wadsworthia): Implicated in gut barrier dysfunction, systemic inflammation, and carcinogenesis.

  • Fungal Overgrowth (Candida spp., Aspergillus spp.): Linked to SIFO/LIFO, contributing to gut inflammation, leaky gut, and immune dysregulation.

Disease Correlation

• Autoimmune Diseases: Dysbiosis and microbial metabolites like lipopolysaccharides (LPS) and mycotoxins trigger immune activation in conditions like rheumatoid arthritis, psoriasis, and lupus.

• Metabolic Syndrome: Methanogens and microbial byproducts influence insulin resistance, obesity, and systemic inflammation, even in the absence of SIBO.

• Cancer: Hydrogen sulfide, LPS, and fungal toxins contribute to chronic inflammation, DNA damage, and tumorigenesis, particularly in gastrointestinal cancers.

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​​​Intestinal-Inflammatory Health Markers (Maximum: 10 points)

This section evaluates biomarkers of intestinal integrity, inflammation, and metabolic processes. These markers remain critical for assessing dysbiosis-related conditions regardless of SIBO test results.

Markers Assessed

1. Calprotectin: Indicates intestinal inflammation; elevated levels are common in IBD and colorectal cancer.

2. Zonulin: Elevated levels suggest intestinal permeability ("leaky gut"), facilitating systemic inflammation.

3. Secretory IgA (sIgA): Low levels compromise mucosal immunity, increasing susceptibility to fungal infections (SIFO/LIFO) and bacterial overgrowth.

4. C-Reactive Protein (CRP): Marker of systemic inflammation, reflecting immune activation.

5. Erythrocyte Sedimentation Rate (ESR): Marker of systemic inflammation, reflecting immune activation.

6. Beta-Glucuronidase: Elevated levels impair detoxification and promote hormone recirculation, contributing to hormone-driven cancers and metabolic dysfunction.

7. Elastase: Low levels reflect pancreatic insufficiency, contributing to malabsorption and nutrient deficiencies.

8. Steatocrit: Reflects fat malabsorption, often exacerbated by fungal overgrowth or large intestinal dysbiosis.

9. Anti-gliadin: May suggest gluten sensitivty or celiac disease

10. Occult Blood: Detects the presence of blood in stools which may be suggestive of active inflammation or underlying disease process that warrants investigation (autoimmunity? cancer?).

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Clinical Symptoms in the (Maximum: 10 points
The Microbiome Concordance Index assesses clinical symptoms, each contributing 1 point to a total of 10 points, to identify systemic and gastrointestinal effects of dysbiosis.

1. Diarrhea: Frequent, loose stools, common in hydrogen-dominant SIBO or SIFO.

2. Constipation: Difficult bowel movements, linked to methane-dominant IMO or fungal overgrowth.

3. Bloating: Abdominal fullness due to gas production in dysbiosis.

4. Belching: Excessive gas from the stomach, often with delayed gastric emptying.

5. Flatulence: Gas expelled rectally, indicating microbial fermentation imbalance.

6. Abdominal Discomfort: Pain or cramping tied to inflammation or motility issues.

7. Acid Reflux: Burning sensation linked to upper GI dysbiosis.

8. Nausea: Discomfort related to microbial toxin release or gastroparesis.

9. Weight Changes: Loss from malabsorption or gain from metabolic dysfunction.

10. Extraintestinal Symptoms: Systemic effects like skin issues, fatigue, joint pain, brain fog, or hormonal imbalances.

 

This symptom-based scoring captures both local and systemic impacts of dysbiosis, even in patients with negative SIBO tests.

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The Value of Monitoring the Microbiome Concordance Index Score Over Time
The Microbiome Concordance Index Score (MCIS) provides a comprehensive, quantifiable framework for evaluating the role of microbiome dysfunction in systemic and gastrointestinal health. By integrating findings from the GI MAP, SIBO breath test, intestinal health markers, and clinical symptoms, the MCIS not only facilitates diagnosis but also serves as a valuable tool for monitoring disease progression and treatment efficacy over time.

Tracking the MCIS allows healthcare providers to:

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Assess Disease Dynamics: Changes in the score can reveal how microbial imbalances, intestinal health, and systemic symptoms evolve, offering a clearer picture of the underlying disease processes, whether they involve autoimmunity, metabolic syndrome, or cancer.

Evaluate Treatment Response: A declining MCIS suggests successful intervention, such as targeted antimicrobial therapy, dietary changes, or probiotic use, in restoring gut balance and reducing systemic inflammation.
Predict Outcomes: Persistent elevations or worsening scores may indicate unresolved dysbiosis or the progression of systemic conditions, enabling early intervention to mitigate risks.
Personalize Care: Insights from the score allow providers to refine treatment strategies, addressing specific dysbiosis patterns, nutrient deficiencies, or systemic inflammatory drivers.

By offering a dynamic, data-driven approach, the MCIS empowers providers to monitor the interconnected nature of gut health and systemic disease, advancing precision medicine and improving long-term patient outcomes.​